Resolving the 180-degree ambiguity in vector magnetic field measurements: The 'minimum' energy solution

Science.gov (United States)

Metcalf, Thomas R.

1994-01-01

I present a robust algorithm that resolves the 180-deg ambiguity in measurements of the solar vector magnetic field. The technique simultaneously minimizes both the divergence of the magnetic field and the electric current density using a simulated annealing algorithm. This results in the field orientation with approximately minimum free energy. The technique is well-founded physically and is simple to implement.

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.

On the chromatic number of triangle-free graphs of large minimum degree

DEFF Research Database (Denmark)

Thomassen, Carsten

2002-01-01

We prove that, for each. fixed real number c > 1/3, the triangle-free graphs of minimum degree at least cn (where n is the number of vertices) have bounded chromatic number. This problem was raised by Erdos and Simonovits in 1973 who pointed out that there is no such result for c <1/3.......We prove that, for each. fixed real number c > 1/3, the triangle-free graphs of minimum degree at least cn (where n is the number of vertices) have bounded chromatic number. This problem was raised by Erdos and Simonovits in 1973 who pointed out that there is no such result for c

Glassy slags as novel waste forms for remediating mixed wastes with high metal contents

International Nuclear Information System (INIS)

Feng, X.; Wronkiewicz, D.J.; Bates, J.K.; Brown, N.R.; Buck, E.C.; Gong, M.; Ebert, W.L.

1994-01-01

Argonne National Laboratory (ANL) is developing a glassy slag final waste form for the remediation of low-level radioactive and mixed wastes with high metal contents. This waste form is composed of various crystalline and metal oxide phases embedded in a silicate glass phase. This work indicates that glassy slag shows promise as final waste form because (1) it has similar or better chemical durability than high-level nuclear waste (HLW) glasses, (2) it can incorporate large amounts of metal wastes, (3) it can incorporate waste streams having low contents of flux components (boron and alkalis), (4) it has less stringent processing requirements (e.g., viscosity and electric conductivity) than glass waste forms, (5) its production can require little or no purchased additives, which can result in greater reduction in waste volume and overall treatment costs. By using glassy slag waste forms, minimum additive waste stabilization approach can be applied to a much wider range of waste streams than those amenable only to glass waste forms

Principle of Minimum Energy in Magnetic Reconnection in a Self-organized Critical Model for Solar Flares

Science.gov (United States)

Farhang, Nastaran; Safari, Hossein; Wheatland, Michael S.

2018-05-01

Solar flares are an abrupt release of magnetic energy in the Sun’s atmosphere due to reconnection of the coronal magnetic field. This occurs in response to turbulent flows at the photosphere that twist the coronal field. Similar to earthquakes, solar flares represent the behavior of a complex system, and expectedly their energy distribution follows a power law. We present a statistical model based on the principle of minimum energy in a coronal loop undergoing magnetic reconnection, which is described as an avalanche process. We show that the distribution of peaks for the flaring events in this self-organized critical system is scale-free. The obtained power-law index of 1.84 ± 0.02 for the peaks is in good agreement with satellite observations of soft X-ray flares. The principle of minimum energy can be applied for general avalanche models to describe many other phenomena.

Surface oxidation in glassy arsenic trisulphide induced by high-energy γ-irradiation

International Nuclear Information System (INIS)

Shpotyuk, M.; Shpotyuk, O.; Serkiz, R.; Demchenko, P.; Kozhyukhin, S.

2014-01-01

Influence of high-energy γ-irradiation with ∼3 MGy dose on glassy g-As 2 S 3 was investigated by a complex of scanning electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction methods. A white layer composed of separate 1–2 μm rhombohedral arsenolite As 2 O 3 crystallites was observed at the surface of γ-irradiated samples. These As 2 O 3 extractions along with crystallised S allotropes are responsible for expansion of the first sharp diffraction peaks in the XRD patterns of g-As 2 S 3 . - Highlights: • As 2 O 3 crystallites are observed at the surface of γ-irradiated As 2 S 3 samples. • Observed crystallites can be removed from the surface after washing and polishing. • γ-Irradiation broadens the FSDP due to satellite lines located on its both sides. • As 2 O 3 and S phases extracted at the surface are responsible for satellite lines

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 ...

Grain-boundary, glassy-phase identification and possible artifacts

International Nuclear Information System (INIS)

Simpson, Y.K.; Carter, C.B.; Sklad, P.; Bentley, J.

1985-01-01

Specimen artifacts such as grain boundary grooving, surface damage of the specimen, and Si contamination are shown experimentally to arise from the ion milling used in the preparation of transmission electron microscopy specimens. These artifacts in polycrystalline, ceramic specimens can cause clean grain boundaries to appear to contain a glassy phase when the dark-field diffuse scattering technique, the Fresnel fringe technique, and analytical electron microscopy (energy dispersive spectroscopy) are used to identify glassy phases at a grain boundary. The ambiguity in interpreting each of these techniques due to the ion milling artifacts will be discussed from a theoretical view point and compared to experimental results obtained for alumina

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.

Design for minimum energy in interstellar communication

Science.gov (United States)

Messerschmitt, David G.

2015-02-01

Microwave digital communication at interstellar distances is the foundation of extraterrestrial civilization (SETI and METI) communication of information-bearing signals. Large distances demand large transmitted power and/or large antennas, while the propagation is transparent over a wide bandwidth. Recognizing a fundamental tradeoff, reduced energy delivered to the receiver at the expense of wide bandwidth (the opposite of terrestrial objectives) is advantageous. Wide bandwidth also results in simpler design and implementation, allowing circumvention of dispersion and scattering arising in the interstellar medium and motion effects and obviating any related processing. The minimum energy delivered to the receiver per bit of information is determined by cosmic microwave background alone. By mapping a single bit onto a carrier burst, the Morse code invented for the telegraph in 1836 comes closer to this minimum energy than approaches used in modern terrestrial radio. Rather than the terrestrial approach of adding phases and amplitudes increases information capacity while minimizing bandwidth, adding multiple time-frequency locations for carrier bursts increases capacity while minimizing energy per information bit. The resulting location code is simple and yet can approach the minimum energy as bandwidth is expanded. It is consistent with easy discovery, since carrier bursts are energetic and straightforward modifications to post-detection pattern recognition can identify burst patterns. Time and frequency coherence constraints leading to simple signal discovery are addressed, and observations of the interstellar medium by transmitter and receiver constrain the burst parameters and limit the search scope.

Minimum energy control and optimal-satisfactory control of Boolean control network

International Nuclear Information System (INIS)

Li, Fangfei; Lu, Xiwen

2013-01-01

In the literatures, to transfer the Boolean control network from the initial state to the desired state, the expenditure of energy has been rarely considered. Motivated by this, this Letter investigates the minimum energy control and optimal-satisfactory control of Boolean control network. Based on the semi-tensor product of matrices and Floyd's algorithm, minimum energy, constrained minimum energy and optimal-satisfactory control design for Boolean control network are given respectively. A numerical example is presented to illustrate the efficiency of the obtained results.

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

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.

Experimental investigations of the minimum ignition energy and the minimum ignition temperature of inert and combustible dust cloud mixtures

Energy Technology Data Exchange (ETDEWEB)

Addai, Emmanuel Kwasi, E-mail: emmanueladdai41@yahoo.com; Gabel, Dieter; Krause, Ulrich

2016-04-15

Highlights: • Ignition sensitivity of a highly flammable dust decreases upon addition of inert dust. • Minimum ignition temperature of a highly flammable dust increases when inert concentration increase. • Minimum ignition energy of a highly flammable dust increases when inert concentration increase. • The permissible range for the inert mixture to minimize the ignition risk lies between 60 to 80%. - Abstract: The risks associated with dust explosions still exist in industries that either process or handle combustible dust. This explosion risk could be prevented or mitigated by applying the principle of inherent safety (moderation). This is achieved by adding an inert material to a highly combustible material in order to decrease the ignition sensitivity of the combustible dust. The presented paper deals with the experimental investigation of the influence of adding an inert dust on the minimum ignition energy and the minimum ignition temperature of the combustible/inert dust mixtures. The experimental investigation was done in two laboratory scale equipment: the Hartmann apparatus and the Godbert-Greenwald furnace for the minimum ignition energy and the minimum ignition temperature test respectively. This was achieved by mixing various amounts of three inert materials (magnesium oxide, ammonium sulphate and sand) and six combustible dusts (brown coal, lycopodium, toner, niacin, corn starch and high density polyethylene). Generally, increasing the inert materials concentration increases the minimum ignition energy as well as the minimum ignition temperatures until a threshold is reached where no ignition was obtained. The permissible range for the inert mixture to minimize the ignition risk lies between 60 to 80%.

Experimental investigations of the minimum ignition energy and the minimum ignition temperature of inert and combustible dust cloud mixtures

International Nuclear Information System (INIS)

Addai, Emmanuel Kwasi; Gabel, Dieter; Krause, Ulrich

2016-01-01

Highlights: • Ignition sensitivity of a highly flammable dust decreases upon addition of inert dust. • Minimum ignition temperature of a highly flammable dust increases when inert concentration increase. • Minimum ignition energy of a highly flammable dust increases when inert concentration increase. • The permissible range for the inert mixture to minimize the ignition risk lies between 60 to 80%. - Abstract: The risks associated with dust explosions still exist in industries that either process or handle combustible dust. This explosion risk could be prevented or mitigated by applying the principle of inherent safety (moderation). This is achieved by adding an inert material to a highly combustible material in order to decrease the ignition sensitivity of the combustible dust. The presented paper deals with the experimental investigation of the influence of adding an inert dust on the minimum ignition energy and the minimum ignition temperature of the combustible/inert dust mixtures. The experimental investigation was done in two laboratory scale equipment: the Hartmann apparatus and the Godbert-Greenwald furnace for the minimum ignition energy and the minimum ignition temperature test respectively. This was achieved by mixing various amounts of three inert materials (magnesium oxide, ammonium sulphate and sand) and six combustible dusts (brown coal, lycopodium, toner, niacin, corn starch and high density polyethylene). Generally, increasing the inert materials concentration increases the minimum ignition energy as well as the minimum ignition temperatures until a threshold is reached where no ignition was obtained. The permissible range for the inert mixture to minimize the ignition risk lies between 60 to 80%.

Ferromagnetic bulk glassy alloys

International Nuclear Information System (INIS)

Inoue, Akihisa; Makino, Akihiro; Mizushima, Takao

2000-01-01

This paper deals with the review on the formation, thermal stability and magnetic properties of the Fe-based bulk glassy alloys in as-cast bulk and melt-spun ribbon forms. A large supercooled liquid region over 50 K before crystallization was obtained in Fe-(Al, Ga)-(P, C, B, Si), Fe-(Cr, Mo, Nb)-(Al, Ga)-(P, C, B) and (Fe, Co, Ni)-Zr-M-B (M=Ti, Hf, V, Nb, Ta, Cr, Mo and W) systems and bulk glassy alloys were produced in a thickness range below 2 mm for the Fe-(Al, Ga)-(P, C, B, Si) system and 6 mm for the Fe-Co-(Zr, Nb, Ta)-(Mo, W)-B system by copper-mold casting. The ring-shaped glassy Fe-(Al, Ga)-(P, C, B, Si) alloys exhibit much better soft magnetic properties as compared with the ring-shaped alloy made from the melt-spun ribbon because of the formation of the unique domain structure. The good combination of high glass-forming ability and good soft magnetic properties indicates the possibility of future development as a new bulk glassy magnetic material

Minimum wall pressure coefficient of orifice plate energy dissipater

Directory of Open Access Journals (Sweden)

Wan-zheng Ai

2015-01-01

Full Text Available Orifice plate energy dissipaters have been successfully used in large-scale hydropower projects due to their simple structure, convenient construction procedure, and high energy dissipation ratio. The minimum wall pressure coefficient of an orifice plate can indirectly reflect its cavitation characteristics: the lower the minimum wall pressure coefficient is, the better the ability of the orifice plate to resist cavitation damage is. Thus, it is important to study the minimum wall pressure coefficient of the orifice plate. In this study, this coefficient and related parameters, such as the contraction ratio, defined as the ratio of the orifice plate diameter to the flood-discharging tunnel diameter; the relative thickness, defined as the ratio of the orifice plate thickness to the tunnel diameter; and the Reynolds number of the flow through the orifice plate, were theoretically analyzed, and their relationships were obtained through physical model experiments. It can be concluded that the minimum wall pressure coefficient is mainly dominated by the contraction ratio and relative thickness. The lower the contraction ratio and relative thickness are, the larger the minimum wall pressure coefficient is. The effects of the Reynolds number on the minimum wall pressure coefficient can be neglected when it is larger than 105. An empirical expression was presented to calculate the minimum wall pressure coefficient in this study.

A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method

Science.gov (United States)

Yoshida, Norio

2018-05-01

A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example.

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.

Solution for Nonlinear Three-Dimensional Intercept Problem with Minimum Energy

Directory of Open Access Journals (Sweden)

Henzeh Leeghim

2013-01-01

a minimum-energy application, which then generates both the desired initial interceptor velocity and the TOF for the minimum-energy transfer. The optimization problem is formulated by using the classical Lagrangian f and g coefficients, which map initial position and velocity vectors to future times, and a universal time variable x. A Newton-Raphson iteration algorithm is introduced for iteratively solving the problem. A generalized problem formulation is introduced for minimizing the TOF as part of the optimization problem. Several examples are presented, and the results are compared with the Hohmann transfer solution approaches. The resulting minimum-energy intercept solution algorithm is expected to be broadly useful as a starting iterative for applications spanning: targeting, rendezvous, interplanetary trajectory design, and so on.

Parameters Tuning of Model Free Adaptive Control Based on Minimum Entropy

Institute of Scientific and Technical Information of China (English)

Chao Ji; Jing Wang; Liulin Cao; Qibing Jin

2014-01-01

Dynamic linearization based model free adaptive control(MFAC) algorithm has been widely used in practical systems, in which some parameters should be tuned before it is successfully applied to process industries. Considering the random noise existing in real processes, a parameter tuning method based on minimum entropy optimization is proposed,and the feature of entropy is used to accurately describe the system uncertainty. For cases of Gaussian stochastic noise and non-Gaussian stochastic noise, an entropy recursive optimization algorithm is derived based on approximate model or identified model. The extensive simulation results show the effectiveness of the minimum entropy optimization for the partial form dynamic linearization based MFAC. The parameters tuned by the minimum entropy optimization index shows stronger stability and more robustness than these tuned by other traditional index,such as integral of the squared error(ISE) or integral of timeweighted absolute error(ITAE), when the system stochastic noise exists.

Using the minimum principle for the Helmholtz free energy in the analysis of the equilibria of a van der Waals fluid

International Nuclear Information System (INIS)

Ascoli, Sergio; Malvestuto, Vincenzo

2004-01-01

For a fluid system, obeying a state equation of the van der Waals type, the gas and the liquid phases can coexist in equilibrium, at a given temperature, only if the volume of the system is kept fixed. Thus, in order to study the two-phase equilibria of a fluid system, it seemed quite natural to choose the molar volume as the independent variable, and, consequently, the Helmholtz free energy as the proper thermodynamic potential for the application of the minimum principle. Specific computations are here carried out for a single van der Waals fluid, namely, pure water at 300 0 C. As a result, the present treatment indicates a simple and effective way to identify the whole range of molar volumes where the equilibrium preferred by the system is a two-phase equilibrium. This range results to be wider than the interval of strict instability of the van der Waals isotherm. Finally, it is pointed out that all the results, obtained here for the van der Waals state equation, can be extended to all the state equations of the same type

Experimental investigations of the minimum ignition energy and the minimum ignition temperature of inert and combustible dust cloud mixtures.

Science.gov (United States)

Addai, Emmanuel Kwasi; Gabel, Dieter; Krause, Ulrich

2016-04-15

The risks associated with dust explosions still exist in industries that either process or handle combustible dust. This explosion risk could be prevented or mitigated by applying the principle of inherent safety (moderation). This is achieved by adding an inert material to a highly combustible material in order to decrease the ignition sensitivity of the combustible dust. The presented paper deals with the experimental investigation of the influence of adding an inert dust on the minimum ignition energy and the minimum ignition temperature of the combustible/inert dust mixtures. The experimental investigation was done in two laboratory scale equipment: the Hartmann apparatus and the Godbert-Greenwald furnace for the minimum ignition energy and the minimum ignition temperature test respectively. This was achieved by mixing various amounts of three inert materials (magnesium oxide, ammonium sulphate and sand) and six combustible dusts (brown coal, lycopodium, toner, niacin, corn starch and high density polyethylene). Generally, increasing the inert materials concentration increases the minimum ignition energy as well as the minimum ignition temperatures until a threshold is reached where no ignition was obtained. The permissible range for the inert mixture to minimize the ignition risk lies between 60 to 80%. Copyright © 2016 Elsevier B.V. All rights reserved.

Binary cluster collision dynamics and minimum energy conformations

Energy Technology Data Exchange (ETDEWEB)

Muñoz, Francisco [Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle (Germany); Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Rogan, José; Valdivia, J.A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Varas, A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Nano-Bio Spectroscopy Group, ETSF Scientific Development Centre, Departamento de Física de Materiales, Universidad del País Vasco UPV/EHU, Av. Tolosa 72, E-20018 San Sebastián (Spain); Kiwi, Miguel, E-mail: m.kiwi.t@gmail.com [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile)

2013-10-15

The collision dynamics of one Ag or Cu atom impinging on a Au{sub 12} cluster is investigated by means of DFT molecular dynamics. Our results show that the experimentally confirmed 2D to 3D transition of Au{sub 12}→Au{sub 13} is mostly preserved by the resulting planar Au{sub 12}Ag and Au{sub 12}Cu minimum energy clusters, which is quite remarkable in view of the excess energy, well larger than the 2D–3D potential barrier height. The process is accompanied by a large s−d hybridization and charge transfer from Au to Ag or Cu. The dynamics of the collision process mainly yields fusion of projectile and target, however scattering and cluster fragmentation also occur for large energies and large impact parameters. While Ag projectiles favor fragmentation, Cu favors scattering due to its smaller mass. The projectile size does not play a major role in favoring the fragmentation or scattering channels. By comparing our collision results with those obtained by an unbiased minimum energy search of 4483 Au{sub 12}Ag and 4483 Au{sub 12}Cu configurations obtained phenomenologically, we find that there is an extra bonus: without increase of computer time collisions yield the planar lower energy structures that are not feasible to obtain using semi-classical potentials. In fact, we conclude that phenomenological potentials do not even provide adequate seeds for the search of global energy minima for planar structures. Since the fabrication of nanoclusters is mainly achieved by synthesis or laser ablation, the set of local minima configurations we provide here, and their distribution as a function of energy, are more relevant than the global minimum to analyze experimental results obtained at finite temperatures, and is consistent with the dynamical coexistence of 2D and 3D liquid Au clusters conformations obtained previously.

Improved initial guess for minimum energy path calculations

International Nuclear Information System (INIS)

Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt; Jónsson, Hannes

2014-01-01

A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used

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

Irradiation-induced defects in graphite and glassy carbon studied by positron annihilation

International Nuclear Information System (INIS)

Hasegawa, M.; Kajino, M.; Kuwahara, H.; Yamaguchi, S.; Kuramoto, E.; Takenaka, M.

1992-01-01

ACAR and positron lifetime measurements have been made on, HOPG, isotropic fine-grained graphites, glassy carbons and C 60 /C 70 . HOPG showed a marked bimodal ACAR distribution along the c-axis. By irradiation of 1.0 X 10 19 fast neutrons/cm 2 remarkable narrowing in the ACAR curves and disappearance of the bimodal distribution were observed. Lifetime in HOPG increased from 225 psec to 289 psec (positron-lifetime in vacancies and their small clusters) by the irradiation. The irradiation on isotropic graphites and glassy carbons, however, gave slight narrowing in ACAR curves and decrease in lifetimes (360 psec → 300psec). This suggests irradiation-induced vacancy trapping in crystallites. In C 60 /C 70 powder two lifetime components were detected: τ 1 =177psec, τ 2 =403psec (I 2 =58%). The former is less than the bulk lifetime of HOPG, while the latter being very close to lifetimes in the isotropic graphites and glassy carbons. This and recent 2D-ACAR study of HOPG surface [15] strongly suggest free and defect surface states around ''soccer ball'' cages

Bistable minimum energy structures (BiMES) for binary robotics

International Nuclear Information System (INIS)

Follador, M; Conn, A T; Rossiter, J

2015-01-01

Bistable minimum energy structures (BiMES) are devices derived from the union of the concepts of dielectric elastomer minimum energy structures and bistable systems. This article presents this novel approach to active, elastic and bistable structures. BiMES are based on dielectric elastomer actuators (DEAs), which act as antagonists and provide the actuation for switching between the two equilibrium positions. A central elastic beam is the backbone of the structure and is buckled into the minimum energy configurations by the action of the two DEAs. The theory and the model of the device are presented, and also its fabrication process. BiMES are considered as fundamental units for more complex structures, which are presented and fabricated as proof of concept. Two different ways of combining the multiple units are proposed: a parallel configuration, to make a simple gripper, and a serial configuration, to generate a binary device. The possibility of using the bistable system as a continuous bender actuator, by modulating the actuation voltage of the two DEAs, was also investigated. (paper)

Energy and environmental norms on Minimum Vital Flux

International Nuclear Information System (INIS)

Maran, S.

2008-01-01

By the end of the year will come into force the recommendations on Minimum Vital flow and operators of hydroelectric power plants will be required to make available part of water of their derivations in order to protect river ecosystems. In this article the major energy and environmental consequences of these rules, we report some quantitative evaluations and are discusses the proposals for overcoming the weaknesses of the approach in the estimation of Minimum Vital Flux [it

Glassy carbon coated graphite for nuclear applications

International Nuclear Information System (INIS)

Delpeux S; Cacciaguerra T; Duclaux L

2005-01-01

Taking into account the problems caused by the treatment of nuclear wastes, the molten salts breeder reactors are expected to a great development. They use a molten fluorinated salt (mixture of LiF, BeF 2 , ThF 4 , and UF 4 ) as fuel and coolant. The reactor core, made of graphite, is used as a neutrons moderator. Despite of its compatibility with nuclear environment, it appears crucial to improve the stability and inertness of graphite against the diffusion of chemicals species leading to its corrosion. One way is to cover the graphite surface by a protective impermeable deposit made of glassy carbon obtained by the pyrolysis of phenolic resin or polyvinyl chloride precursors. The main difficulty in the synthesis of glassy carbon is to create exclusively, in the primary pyrolysis product, a micro-porosity of about twenty Angstroms which closes later at higher temperature. Therefore, the evacuation of the volatile products occurring mainly between 330 and 600 C, must progress slowly to avoid the material to crack. In this study, the optimal parameters for the synthesis of glassy carbon as well as glassy carbon deposits on nuclear-type graphite pieces are discussed. Both thermal treatment of phenolic and PVC resins have been performed. The structure and micro-texture of glassy carbon have been investigated by X-ray diffraction, scanning and transmission electron microscopies and helium pycno-metry. Glassy carbon samples (obtained at 1200 C) show densities ranging from 1.3 to 1.55 g/cm 3 and closed pores with nano-metric size (∼ 5 to 10 nm) appear clearly on the TEM micrographs. Then, a thermal treatment to 2700 C leads to the shrinkage of the entangled graphene ribbons, in good agreement with the proposed texture model for glassy carbon. Glassy carbon deposits on nuclear graphite have been developed by an impregnation method. The uniformity of the deposit depends clearly on the surface texture and the chemistry of the graphite substrate. The deposit regions where

Glassy carbon coated graphite for nuclear applications

Energy Technology Data Exchange (ETDEWEB)

Delpeux, S.; Cacciaguerra, T.; Duclaux, L. [Orleans Univ., CRMD, CNRS, 45 (France)

2005-07-01

Taking into account the problems caused by the treatment of nuclear wastes, the molten salts breeder reactors are expected to a great development. They use a molten fluorinated salt (mixture of LiF, BeF{sub 2}, ThF{sub 4}, and UF{sub 4}) as fuel and coolant. The reactor core, made of graphite, is used as a neutrons moderator. Despite of its compatibility with nuclear environment, it appears crucial to improve the stability and inertness of graphite against the diffusion of chemicals species leading to its corrosion. One way is to cover the graphite surface by a protective impermeable deposit made of glassy carbon obtained by the pyrolysis of phenolic resin [1,2] or polyvinyl chloride [3] precursors. The main difficulty in the synthesis of glassy carbon is to create exclusively, in the primary pyrolysis product, a micro-porosity of about twenty Angstroms which closes later at higher temperature. Therefore, the evacuation of the volatile products occurring mainly between 330 and 600 C, must progress slowly to avoid the material to crack. In this study, the optimal parameters for the synthesis of glassy carbon as well as glassy carbon deposits on nuclear-type graphite pieces are discussed. Both thermal treatment of phenolic and PVC resins have been performed. The structure and micro-texture of glassy carbon have been investigated by X-ray diffraction, scanning and transmission electron microscopies and helium pycno-metry. Glassy carbon samples (obtained at 1200 C) show densities ranging from 1.3 to 1.55 g/cm{sup 3} and closed pores with nano-metric size ({approx} 5 to 10 nm) appear clearly on the TEM micrographs. Then, a thermal treatment to 2700 C leads to the shrinkage of the entangled graphene ribbons (Fig 1), in good agreement with the proposed texture model for glassy carbon (Fig 2) [4]. Glassy carbon deposits on nuclear graphite have been developed by an impregnation method. The uniformity of the deposit depends clearly on the surface texture and the chemistry

Bounds on Minimum Energy per Bit for Optical Wireless Relay Channels

Directory of Open Access Journals (Sweden)

A. D. Raza

2014-09-01

Full Text Available An optical wireless relay channel (OWRC is the classical three node network consisting of source, re- lay and destination nodes with optical wireless connectivity. The channel law is assumed Gaussian. This paper studies the bounds on minimum energy per bit required for reliable communication over an OWRC. It is shown that capacity of an OWRC is concave and energy per bit is monotonically increasing in square of the peak optical signal power, and consequently the minimum energy per bit is inversely pro- portional to the square root of asymptotic capacity at low signal to noise ratio. This has been used to develop upper and lower bound on energy per bit as a function of peak signal power, mean to peak power ratio, and variance of channel noise. The upper and lower bounds on minimum energy per bit derived in this paper correspond respectively to the decode and forward lower bound and the min-max cut upper bound on OWRC capacity

A wrinkling-based method for investigating glassy polymer film relaxation as a function of film thickness and temperature.

Science.gov (United States)

Chung, Jun Young; Douglas, Jack F; Stafford, Christopher M

2017-10-21

We investigate the relaxation dynamics of thin polymer films at temperatures below the bulk glass transition T g by first compressing polystyrene films supported on a polydimethylsiloxane substrate to create wrinkling patterns and then observing the slow relaxation of the wrinkled films back to their final equilibrium flat state by small angle light scattering. As with recent relaxation measurements on thin glassy films reported by Fakhraai and co-workers, we find the relaxation time of our wrinkled films to be strongly dependent on film thickness below an onset thickness on the order of 100 nm. By varying the temperature between room temperature and T g (≈100 °C), we find that the relaxation time follows an Arrhenius-type temperature dependence to a good approximation at all film thicknesses investigated, where both the activation energy and the relaxation time pre-factor depend appreciably on film thickness. The wrinkling relaxation curves tend to cross at a common temperature somewhat below T g , indicating an entropy-enthalpy compensation relation between the activation free energy parameters. This compensation effect has also been observed recently in simulated supported polymer films in the high temperature Arrhenius relaxation regime rather than the glassy state. In addition, we find that the film stress relaxation function, as well as the height of the wrinkle ridges, follows a stretched exponential time dependence and the short-time effective Young's modulus derived from our modeling decreases sigmoidally with increasing temperature-both characteristic features of glassy materials. The relatively facile nature of the wrinkling-based measurements in comparison to other film relaxation measurements makes our method attractive for practical materials development, as well as fundamental studies of glass formation.

Minimum detection efficiency for the loophole-free confirmation of quantum contextuality

International Nuclear Information System (INIS)

Xiang Yang; Hong Fang-Yu

2013-01-01

Klyachko—Can—Binicioğlu—Shumovsky (KCBS) inequality is a Bell-like inequality, the violation of which can be used to confirm the existence of quantum contextuality. However, the imperfection of detection efficiency may cause the so-called loophole in actual KCBS's experiments. We derive an alternative KCBS inequality to deal with the loophole in actual KCBS's experiments. We prove that if the experimental data violate this KCBS inequality, the loophole-free violation of the original KCBS inequality will occur. We show that the minimum detection efficiency needed for a loophole-free violation of the KCBS inequality is about 0.9738

Operation of low-energy ion implanters for Si, N, C ion implantation into silicon and glassy carbon

International Nuclear Information System (INIS)

Carder, D.A.; Markwitz, A.

2009-01-01

This report details the operation of the low-energy ion implanters at GNS Science for C, N and Si implantations. Two implanters are presented, from a description of the components through to instructions for operation. Historically the implanters have been identified with the labels 'industrial' and 'experimental'. However, the machines only differ significantly in the species of ions available for implantation and sample temperature during implantation. Both machines have been custom designed for research purposes, with a wide range of ion species available for ion implantation and the ability to implant two ions into the same sample at the same time from two different ion sources. A fast sample transfer capability and homogenous scanning profiles are featured in both cases. Samples up to 13 mm 2 can be implanted, with the ability to implant at temperatures down to liquid nitrogen temperatures. The implanters have been used to implant 28 Si + , 14 N + and 12 C + into silicon and glassy carbon substrates. Rutherford backscattering spectroscopy has been used to analyse the implanted material. From the data a Si 30 C 61 N 9 layer was measured extending from the surface to a depth of about 77 ± 2 nm for (100) silicon implanted with 12 C + and 14 N + at multiple energies. Silicon and nitrogen ion implantation into glassy carbon produced a Si (40.5 %), C (38 %), N (19.5 %) and O (2%) layer centred around a depth of 50 ± 2 nm from the surface. (author). 8 refs., 20 figs

Glassy slag: A complementary waste form to homogeneous glass for the implementation of MAWS in treating DOE low level/mixed wastes

International Nuclear Information System (INIS)

Feng, X.; Ordaz, G.; Krumrine, P.

1994-01-01

Glassy slag waste forms are being developed to complement glass waste forms in implementing the Minimum Additive Waste Stabilization (MAWS) Program for supporting DOE's environmental restoration efforts. These glassy slags are composed of various metal oxide crystalline phases embedded in an alumino-silicate glass phase. The slags are appropriate final waste forms for waste streams that contain large amounts of scrap metals and elements with low solubilities in glass, and that have low-flux contents. Homogeneous glass waste forms are appropriate for wastes with sufficient fluxes and low metal contents. Therefore, utilization of both glass and glassy slag waste forms will make vitrification technology applicable to the treatment of a much larger range of radioactive and mixed wastes. The MAWS approach was a plied to glassy slags by blending multiple waste streams to produce the final waste form, minimizing overall waste form volume and reducing costs. The crystalline oxide phases formed in the glassy slags can be specially formulated so that they are very durable and contain hazardous and radioactive elements in their lattice structures. The Structural Bond Strength (SBS) Model was used to predict the chemical durability of the product from the slag composition so that optimized slag compositions could be obtain with a limited number of crucible melts and testing

Thermodynamic picture of the glassy state

NARCIS (Netherlands)

Nieuwenhuizen, T.M.

2000-01-01

A picture for the thermodynamics of the glassy state is introduced. It assumes that one extra parameter, the effective temperature, is needed to describe the glassy state. This explains the classical paradoxes concerning the Ehrenfest relations and the Prigogine-Defay ratio. As a second feature, the

Attainability and minimum energy of multiple-stage cascade membrane Systems

KAUST Repository

Alshehri, Ali

2015-08-12

Process design and simulation of multi-stage membrane systems have been widely studied in many gas separation systems. However, general guidelines have not been developed yet for the attainability and the minimum energy consumption of a multi-stage membrane system. Such information is important for conceptual process design and thus it is the topic of this work. Using a well-mixed membrane model, it was determined that the attainability curve of multi-stage systems is defined by the pressure ratio and membrane selectivity. Using the constant recycle ratio scheme, the recycle ratio can shift the attainability behavior between single-stage and multi-stage membrane systems. When the recycle ratio is zero, all of the multi-stage membrane processes will decay to a single-stage membrane process. When the recycle ratio approaches infinity, the required selectivity and pressure ratio reach their absolute minimum values, which have a simple relationship with that of a single-stage membrane process, as follows: View the MathML sourceSn=S1, View the MathML sourceγn=γ1, where n is the number of stages. The minimum energy consumption of a multi-stage membrane process is primarily determined by the membrane selectivity and recycle ratio. A low recycle ratio can significantly reduce the required membrane selectivity without substantial energy penalty. The energy envelope curve can provide a guideline from an energy perspective to determine the minimum required membrane selectivity in membrane process designs to compete with conventional separation processes, such as distillation.

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.

Material dependence of electron inelastic mean free paths at low energies

International Nuclear Information System (INIS)

Tanuma, S.; Powell, C.J.; Penn, D.R.

1990-01-01

We present and discuss electron inelastic mean free path (IMFP) data for aluminum and gold in the 50--200 eV range. These elements serve as examples of IMFP calculations that have been made for 50--2000 eV electrons in 31 materials (27 elements and 4 compounds). Substantial differences are found in the shapes of the IMFP versus energy curves for Al and Au and these can be understood in terms of the different inelastic scattering mechanisms in the two metals. The minimum IMFP value occurs at 40 eV in aluminum and at 120 eV in gold, a result which is consistent with the trends expected from free-electron IMFP calculations. This result differs, however, from that expected from the Seah and Dench attenuation length formula which shows essentially no material dependence at low energies. We have extended a general formula derived earlier to describe the calculated IMFPs over the 200--2000 eV energy range to give the IMFP dependences on material and energy from 50 to 2000 eV

On the chromatic number of pentagon-free graphs of large minimum degree

DEFF Research Database (Denmark)

Thomassen, Carsten

2007-01-01

We prove that, for each fixed real number c > 0, the pentagon-free graphs of minimum degree at least cn (where n is the number of vertices) have bounded chromatic number. This problem was raised by Erdős and Simonovits in 1973. A similar result holds for any other fixed odd cycle, except the tria...

Energy-minimum sub-threshold self-timed circuits using current-sensing completion detection

DEFF Research Database (Denmark)

Akgun, O. C.; Rodrigues, J. N.; Sparsø, Jens

2011-01-01

This study addresses the design of self-timed energy-minimum circuits, operating in the sub-VT domain and a generic implementation template using bundled-data circuitry and current sensing completion detection (CSCD). Furthermore, a fully decoupled latch controller was developed, which integrates......V. Spice simulations indicate a gain of 52.58% in throughput because of asynchronous operation. By trading the throughput improvement, energy dissipation is reduced by 16.8% at the energy-minimum supply voltage....

Formation of glassy carbon structure and its change under neutron irradiation

Energy Technology Data Exchange (ETDEWEB)

Kurolenkin, E.I.; Lopato, Yu.S.; Virgil' ev, Yu.S.; Khakimova, D.K.; Aksenov, S.I.

1981-01-01

The changes of glassy carbon structure, which is prepared of phenol-formaldehyde and furfurol-phenol-formaldehyde resins in the process of irradiation with 5.3x10/sup 20/ cm/sup -2/ neutron fluence with the energy E>0.18 MeV in the temperature range of 90-540 deg C are studied. It is established the irradiation results in the shrinkage of the samples. The compression of the samples increases with the irradiation temperature and neutron fluence. The thermal annealing does not result in the restoration of the volume of samples. The sample shrinkage, caused by more compact package of globular structures and the destruction of film structures, decrease gas permeability of glassy carbon.

Study of electrical properties of glassy Se100–xTex alloys

Indian Academy of Sciences (India)

Unknown

can be successfully explained by correlated barrier hopping (CBH) model. ... The results show that bipolaron hopping dominates over single-polaron hopping in this glassy system. This .... where ∆E is the activation energy and σ0 is called the.

Energy and IAQ Implications of Alternative Minimum Ventilation Rates in California Retail and School Buildings

Energy Technology Data Exchange (ETDEWEB)

Dutton, Spencer M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Fisk, William J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2015-01-01

For a stand-alone retail building, a primary school, and a secondary school in each of the 16 California climate zones, the EnergyPlus building energy simulation model was used to estimate how minimum mechanical ventilation rates (VRs) affect energy use and indoor air concentrations of an indoor-generated contaminant. The modeling indicates large changes in heating energy use, but only moderate changes in total building energy use, as minimum VRs in the retail building are changed. For example, predicted state-wide heating energy consumption in the retail building decreases by more than 50% and total building energy consumption decreases by approximately 10% as the minimum VR decreases from the Title 24 requirement to no mechanical ventilation. The primary and secondary schools have notably higher internal heat gains than in the retail building models, resulting in significantly reduced demand for heating. The school heating energy use was correspondingly less sensitive to changes in the minimum VR. The modeling indicates that minimum VRs influence HVAC energy and total energy use in schools by only a few percent. For both the retail building and the school buildings, minimum VRs substantially affected the predicted annual-average indoor concentrations of an indoor generated contaminant, with larger effects in schools. The shape of the curves relating contaminant concentrations with VRs illustrate the importance of avoiding particularly low VRs.

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

Analysis of Lead and Zinc by Mercury-Free Potentiometric Stripping Analysis

DEFF Research Database (Denmark)

Andersen, Jens Enevold Thaulov

1997-01-01

A method is presented for trace-element analysis of lead and zinc by potentiometric stripping analysis (PSA) where both the glassy-carbon working electrode and the electrolyte are free of mercury. Analysis of zinc requires an activation procedure of the glassy-carbon electrode. The activation...... is performed by pre-concentrating zinc on glassy carbon at -1400 mV(SCE) in a mercury-free electrolyte containing 0.1 M HCl and 2 ppm Zn2+, followed by stripping at approx. -1050 mV. A linear relationship between stripping peak areas, recorded in the derivative mode, and concentration was found...

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.

Positronics of radiation-induced effects in chalcogenide glassy semiconductors

International Nuclear Information System (INIS)

Shpotyuk, O.; Kozyukhin, S. A.; Shpotyuk, M.; Ingram, A.; Szatanik, R.

2015-01-01

Using As 2 S 3 and AsS 2 glasses as an example, the principal possibility of using positron annihilation spectroscopy methods for studying the evolution of the free volume of hollow nanoobjects in chalcogenide glassy semiconductors exposed to radiation is shown. The results obtained by measurements of the positron annihilation lifetime and Doppler broadening of the annihilation line in reverse chronological order are in full agreement with the optical spectroscopy data in the region of the fundamental absorption edge, being adequately described within coordination defect-formation and physical-aging models

Positronics of radiation-induced effects in chalcogenide glassy semiconductors

Energy Technology Data Exchange (ETDEWEB)

Shpotyuk, O. [Scientific Research Company “Carat” (Ukraine); Kozyukhin, S. A., E-mail: sergkoz@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Shpotyuk, M. [Scientific Research Company “Carat” (Ukraine); Ingram, A. [Opole Technical University (Poland); Szatanik, R. [Opole University (Poland)

2015-03-15

Using As{sub 2}S{sub 3} and AsS{sub 2} glasses as an example, the principal possibility of using positron annihilation spectroscopy methods for studying the evolution of the free volume of hollow nanoobjects in chalcogenide glassy semiconductors exposed to radiation is shown. The results obtained by measurements of the positron annihilation lifetime and Doppler broadening of the annihilation line in reverse chronological order are in full agreement with the optical spectroscopy data in the region of the fundamental absorption edge, being adequately described within coordination defect-formation and physical-aging models.

Cooperative strings and glassy interfaces.

Science.gov (United States)

Salez, Thomas; Salez, Justin; Dalnoki-Veress, Kari; Raphaël, Elie; Forrest, James A

2015-07-07

We introduce a minimal theory of glass formation based on the ideas of molecular crowding and resultant string-like cooperative rearrangement, and address the effects of free interfaces. In the bulk case, we obtain a scaling expression for the number of particles taking part in cooperative strings, and we recover the Adam-Gibbs description of glassy dynamics. Then, by including thermal dilatation, the Vogel-Fulcher-Tammann relation is derived. Moreover, the random and string-like characters of the cooperative rearrangement allow us to predict a temperature-dependent expression for the cooperative length ξ of bulk relaxation. Finally, we explore the influence of sample boundaries when the system size becomes comparable to ξ. The theory is in agreement with measurements of the glass-transition temperature of thin polymer films, and allows quantification of the temperature-dependent thickness hm of the interfacial mobile layer.

Comparison of glassy slag waste forms produced in laboratory crucibles and in a bench-scale plasma furnace

International Nuclear Information System (INIS)

Feng, X.; Wronkiewicz, D.J.; Brown, N.R.; Gong, M.; Whitworth, C.; Filius, K.; Battleson, D.

1994-01-01

Vitrification is currently the best demonstrated available technology for the disposal of high-level radioactive wastes. An innovative vitrification approach known as minimum additive waste stabilization (MAWS) is being developed. Both homogeneous glass and glassy slags have been used in implementing MAWS. Glassy slags (vitro-ceramics) are glass-crystal composites, and they are composed of various metal oxide crystalline phases embedded in an aluminosilicate glass matrix. Glassy slags with compositions developed in crucible melts at Argonne National Laboratory (ANL) were successfully produced in a bench-scale Retech plasma centrifugal furnace (PCF) by MSE, Inc. Detailed examinations of these materials showed that the crucible melts and the PCF produced similar glass and crystalline phases. The two sets of glassy slags exhibited similar chemical durability in terms of normalized releases of their major components. The slags produced in the PCF furnace using metals were usually less oxidized, although this had no effect on the corrosion behavior of the major components of the slags. However, the normalized release rate of cerium was initially lower for the PCF slags. This difference diminished with time as the redox sates of the metal oxides in slags began to be controlled by exposure to air in the tests. Thus, the deference in cerium release due to the differences in slag redox state may be transitory. The cerium solubility is a complex function of redox state and solution pH and Eh

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.

Minimum Energy Requirements in Complex Distillation Arrangements

Energy Technology Data Exchange (ETDEWEB)

Halvorsen, Ivar J

2001-07-01

Distillation is the most widely used industrial separation technology and distillation units are responsible for a significant part of the total heat consumption in the world's process industry. In this work we focus on directly (fully thermally) coupled column arrangements for separation of multicomponent mixtures. These systems are also denoted Petlyuk arrangements, where a particular implementation is the dividing wall column. Energy savings in the range of 20-40% have been reported with ternary feed mixtures. In addition to energy savings, such integrated units have also a potential for reduced capital cost, making them extra attractive. However, the industrial use has been limited, and difficulties in design and control have been reported as the main reasons. Minimum energy results have only been available for ternary feed mixtures and sharp product splits. This motivates further research in this area, and this thesis will hopefully give some contributions to better understanding of complex column systems. In the first part we derive the general analytic solution for minimum energy consumption in directly coupled columns for a multicomponent feed and any number of products. To our knowledge, this is a new contribution in the field. The basic assumptions are constant relative volatility, constant pressure and constant molar flows and the derivation is based on Underwood's classical methods. An important conclusion is that the minimum energy consumption in a complex directly integrated multi-product arrangement is the same as for the most difficult split between any pair of the specified products when we consider the performance of a conventional two-product column. We also present the Vmin-diagram, which is a simple graphical tool for visualisation of minimum energy related to feed distribution. The Vmin-diagram provides a simple mean to assess the detailed flow requirements for all parts of a complex directly coupled arrangement. The main purpose in the first

Minimum Energy Requirements in Complex Distillation Arrangements

Energy Technology Data Exchange (ETDEWEB)

Halvorsen, Ivar J.

2001-07-01

Distillation is the most widely used industrial separation technology and distillation units are responsible for a significant part of the total heat consumption in the world's process industry. In this work we focus on directly (fully thermally) coupled column arrangements for separation of multicomponent mixtures. These systems are also denoted Petlyuk arrangements, where a particular implementation is the dividing wall column. Energy savings in the range of 20-40% have been reported with ternary feed mixtures. In addition to energy savings, such integrated units have also a potential for reduced capital cost, making them extra attractive. However, the industrial use has been limited, and difficulties in design and control have been reported as the main reasons. Minimum energy results have only been available for ternary feed mixtures and sharp product splits. This motivates further research in this area, and this thesis will hopefully give some contributions to better understanding of complex column systems. In the first part we derive the general analytic solution for minimum energy consumption in directly coupled columns for a multicomponent feed and any number of products. To our knowledge, this is a new contribution in the field. The basic assumptions are constant relative volatility, constant pressure and constant molar flows and the derivation is based on Underwood's classical methods. An important conclusion is that the minimum energy consumption in a complex directly integrated multi-product arrangement is the same as for the most difficult split between any pair of the specified products when we consider the performance of a conventional two-product column. We also present the Vmin-diagram, which is a simple graphical tool for visualisation of minimum energy related to feed distribution. The Vmin-diagram provides a simple mean to assess the detailed flow requirements for all parts of a complex directly coupled arrangement. The main purpose in

Minimum beam-energy spread of a high-current rf linac

International Nuclear Information System (INIS)

Chan, K.C.D.; Fraser, J.S.

1987-01-01

Energy spread is an important parameter of an electron linac and, usually, is determined by the time dependence of the external rf accelerating field. By using a combination of fundamental and higher harmonic frequencies, the accelerating field can be maintained approximately constant over a beam bunch with the resultant energy spread approximately zero. This technique is no longer adequate when the longitudinal wake field of the beam bunch is taken into account. The wake-field variation along the bunch length introduces an energy spread that cannot be exactly compensated for with the use of fundamental and higher harmonic frequencies. The achievable minimum energy spread including the wake-field effect is therefore limited. In this paper, we report the minimum energy spreads achievable using the fundamental and third-harmonic frequencies, calculated using a least-squares algorithm, for some typical structures in use at Los Alamos National Laboratory. The dependence of these results on bunch shape, bunch charge, and structure frequency is discussed. Also included are discussions of schemes for implementing the third-harmonic frequency and their effectiveness

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.

Low temperature thermal conductivities of glassy carbons

International Nuclear Information System (INIS)

Anderson, A.C.

1979-01-01

The thermal conductivity of glassy carbon in the temperature range 0.1 to 100 0 K appears to depend only on the temperature at which the material was pyrolyzed. The thermal conductivity can be related to the microscopic structure of glassy carbon. The reticulated structure is especially useful for thermal isolation at cryogenic temperatures

Destruction-polymerization transformations as a source of radiation-induced extended defects in chalcogenide glassy semiconductors

International Nuclear Information System (INIS)

Shpotyuk, Oleh; Filipecki, Jacek; Shpotyuk, Mykhaylo

2013-01-01

Long-wave shift of the optical transmission spectrum in the region of fundamental optical absorption edge is registered for As 2 S 3 chalcogenide glassy semiconductors after γ-irradiation. This effect is explained in the frameworks of the destruction-polymerization transformations concept by accepting the switching of the heteropolar As-S covalent bonds into homopolar As-As ones. It is assumed that (As 4 + ; S 1 - ) defect pairs are created under such switching. Formula to calculate content of the induced defects in chalcogenide glassy semiconductors is proposed. It is assumed that defects concentration depends on energy of broken covalent bond, bond-switching energy balance, correlation energy, optical band-gap and energy of excitation light. It is shown that theoretically calculated maximally possible content of radiation-induced defects in As 2 S 3 is about 1.6% while concentration of native defects is negligible. (copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

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.

Treatment of early glassy cell carcinoma of uterine cervix

International Nuclear Information System (INIS)

Kim, Ok Bae; Kim, Jin Hee; Choi, Tae Jin

2006-01-01

The purpose of this study was to investigate the clinical findings, treatment, and outcome of patients with glassy cell carcinoma of cervix. We reviewed all cases of glassy cell carcinoma of the uterine cervix confirmed and treated at the Dongsan Medical Center, Keimyung University, between January 1993 and December 2005. There were 7 cases with histopathologically confirmed gassy cell carcinoma. A tumor was diagnosed as glassy cell carcinoma if over 50% of the tumor cell type displayed glassy cell features. Six patients with stage IB had radical hysterectomy and bilateral pelvic node dissection, and 2 of them received adjuvant external pelvic irradiation with concurrent chemotherapy. Remaining one patient with stage IIA had curative concurrent chemoradiotherapy with external pelvic irradiation and brachytherapy. There were 7 patients diagnosed as glassy cell carcinoma among the 3,745 (0.2%) patients of carcinoma of uterine cervix. The mean age of 7 patients was 44 years with range of 35 to 53 years of age. The most frequent symptom was vaginal bleeding (86%). By the punch biopsy undertaken before treatment of 7 cases, 2 only cases could diagnose as glassy cell carcinoma of uterine cervix, but remaining of them confirmed by surgical pathological examination. The mean follow up duration was 73 months with range of 13 to 150 months. All 7 patients were alive without disease after treatment. Glassy cell carcinoma of the uterine cervix is a distinct clinicopathologic entity that demonstrates an aggressive biologic behavior. However for early-stage disease, we may have more favorable clinical outcome with radical surgery followed by chemoradiotherapy

EDTA modified glassy carbon electrode: Preparation and characterization

International Nuclear Information System (INIS)

Ustuendag, Zafer; Solak, Ali Osman

2009-01-01

EDTA-phenoxyamide modified glassy carbon electrode (EDTA-GC) was prepared at a glassy carbon electrode by surface synthesis. In the first step, nitrophenyl was grafted to the glassy carbon (GC) surface via the electrochemical reduction of its tetraflouroborate diazonium salt. In the second step, nitrophenyl-modified electrode (NP-GC) was subjected to the cathodic potential scan to reduce the nitro to amine group. p-Aminophenyl modified glassy carbon electrode (AP-GC) was dipped into a EDTA solution containing 1-ethyl-3(3-(dimethlyamino)propyl)-carbodiimide (EDC) as an activating agent. Thus formed ((2-anilino-2-oxoethyl){2-[bis(carboxymethyl)amino]-ethyl}amino)acetic acid modified GC electrode was denoted as EDTA-GC and characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), ellipsometry and X-ray photoelectron spectroscopy (XPS). Complexation of the EDTA-GC surface with Pb 2+ ions was investigated if this electrode could be used as a metal sensor.

Boron ion irradiation induced structural and surface modification of glassy carbon

International Nuclear Information System (INIS)

Kalijadis, Ana; Jovanović, Zoran; Cvijović-Alagić, Ivana; Laušević, Zoran

2013-01-01

The incorporation of boron into glassy carbon was achieved by irradiating two different types of targets: glassy carbon polymer precursor and carbonized glassy carbon. Targets were irradiated with a 45 keV B 3+ ion beam in the fluence range of 5 × 10 15 –5 × 10 16 ions cm −2 . For both types of targets, the implanted boron was located in a narrow region under the surface. Following irradiation, the polymer was carbonized under the same condition as the glassy carbon samples (at 1273 K) and examined by Raman spectroscopy, temperature programmed desorption, hardness and cyclic voltammetry measurements. Structural analysis showed that during the carbonization process of the irradiated polymers, boron is substitutionally incorporated into the glassy carbon structure, while for irradiated carbonized glassy carbon samples, boron irradiation caused an increase of the sp 3 carbon fraction, which is most pronounced for the highest fluence irradiation. Further analyses showed that different nature of boron incorporation, and thus changed structural parameters, are crucial for obtaining glassy carbon samples with modified mechanical, chemical and electrochemical properties over a wide range

Annealing effects on the migration of ion-implanted cadmium in glassy carbon

Energy Technology Data Exchange (ETDEWEB)

Hlatshwayo, T.T., E-mail: thulani.hlatshwayo@up.ac.za [Physics Department, University of Pretoria, Pretoria (South Africa); Sebitla, L.D. [Physics Department, University of Pretoria, Pretoria (South Africa); Physics Department, University of Botswana, Gaborone (Botswana); Njoroge, E.G.; Mlambo, M.; Malherbe, J.B. [Physics Department, University of Pretoria, Pretoria (South Africa)

2017-03-15

The migration behaviour of cadmium (Cd) implanted into glassy carbon and the effects of annealing on radiation damage introduced by ion implantation were investigated. The glassy carbon substrates were implanted with Cd at a dose of 2 × 10{sup 16} ions/cm{sup 2} and energy of 360 keV. The implantation was performed at room temperature (RT), 430 °C and 600 °C. The RT implanted samples were isochronally annealed in vacuum at 350, 500 and 600 °C for 1 h and isothermally annealed at 350 °C up to 4 h. The as-implanted and annealed samples were characterized by Raman spectroscopy and Rutherford backscattering spectrometry (RBS). Raman results revealed that implantation at room temperature amorphized the glassy carbon structure while high temperature implantations resulted in slightly less radiation damage. Isochronal annealing of the RT implanted samples resulted in some recrystallization as a function of increasing temperature. The original glassy carbon structure was not achieved at the highest annealing temperature of 600 °C. Diffusion of Cd in glassy carbon was already taking place during implantation at 430 °C. This diffusion of Cd was accompanied by significant loss from the surface during implantation at 600 °C. Isochronal annealing of the room temperature implanted samples at 350 °C for 1 h caused Cd to diffuse towards the bulk while isothermal annealing at 500 and 600 °C resulted in the migration of implanted Cd toward the surface accompanied by a loss of Cd from the surface. Isothermal annealing at 350 °C for 1 h caused Cd to diffuse towards the bulk while for annealing time >1 h Cd diffused towards the surface. These results were interpreted in terms of trapping and de-trapping of implanted Cd by radiation damage.

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

Temporal disconnectivity of the energy landscape in glassy systems

Science.gov (United States)

Lempesis, Nikolaos; Boulougouris, Georgios C.; Theodorou, Doros N.

2013-03-01

An alternative graphical representation of the potential energy landscape (PEL) has been developed and applied to a binary Lennard-Jones glassy system, providing insight into the unique topology of the system's potential energy hypersurface. With the help of this representation one is able to monitor the different explored basins of the PEL, as well as how - and mainly when - subsets of basins communicate with each other via transitions in such a way that details of the prior temporal history have been erased, i.e., local equilibration between the basins in each subset has been achieved. In this way, apart from detailed information about the structure of the PEL, the system's temporal evolution on the PEL is described. In order to gather all necessary information about the identities of two or more basins that are connected with each other, we consider two different approaches. The first one is based on consideration of the time needed for two basins to mutually equilibrate their populations according to the transition rate between them, in the absence of any effect induced by the rest of the landscape. The second approach is based on an analytical solution of the master equation that explicitly takes into account the entire explored landscape. It is shown that both approaches lead to the same result concerning the topology of the PEL and dynamical evolution on it. Moreover, a "temporal disconnectivity graph" is introduced to represent a lumped system stemming from the initial one. The lumped system is obtained via a specially designed algorithm [N. Lempesis, D. G. Tsalikis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Phys. 135, 204507 (2011), 10.1063/1.3663207]. The temporal disconnectivity graph provides useful information about both the lumped and the initial systems, including the definition of "metabasins" as collections of basins that communicate with each other via transitions that are fast relative to the observation time. Finally, the two examined

Studies on Photodarkening Effect in Glassy As2S3 Using High Field NMR

Science.gov (United States)

Hari, Parameswar; Su, Tining; Taylor, Craig; Reyes, Arneil; Kuhns, Phil; Moulton, William; Sullivan, N. S.

2001-03-01

Photodarkening, or the shift of the optical absorption edge to smaller energies after excitation with light whose energy is near that of the optical band edge, has been studied in many chalcogenide glasses for many years. Recently we have conducted nuclear magnetic resonance (NMR) studies of 75As in glassy As2S3 at 17T . We compared the 75As NMR lineshape in glassy As2S3 before and after irradiation at 77K. After irradiation at 514.5 nm for 230 hours with 170 mW/cm2 there is a subtle change in the NMR lineshape. This change is reversible on annealing at 200 C for 1.75 hours. We will discuss the implications of this result based on NMR lineshape analysis using an exact solution of the spin 3/2 Hamiltonian

EDTA modified glassy carbon electrode: Preparation and characterization

Energy Technology Data Exchange (ETDEWEB)

Ustuendag, Zafer [Dumlupinar University, Faculty of Arts and Sciences, Department of Chemistry, Kuetahya (Turkey); Solak, Ali Osman [Ankara University, Faculty of Science, Department of Chemistry, Degol Street, Tandogan, 06100 Ankara (Turkey)], E-mail: osolak@science.ankara.edu.tr

2009-11-01

EDTA-phenoxyamide modified glassy carbon electrode (EDTA-GC) was prepared at a glassy carbon electrode by surface synthesis. In the first step, nitrophenyl was grafted to the glassy carbon (GC) surface via the electrochemical reduction of its tetraflouroborate diazonium salt. In the second step, nitrophenyl-modified electrode (NP-GC) was subjected to the cathodic potential scan to reduce the nitro to amine group. p-Aminophenyl modified glassy carbon electrode (AP-GC) was dipped into a EDTA solution containing 1-ethyl-3(3-(dimethlyamino)propyl)-carbodiimide (EDC) as an activating agent. Thus formed ((2-anilino-2-oxoethyl){l_brace}2-[bis(carboxymethyl)amino]-ethyl{r_brace}amino)acetic acid modified GC electrode was denoted as EDTA-GC and characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), ellipsometry and X-ray photoelectron spectroscopy (XPS). Complexation of the EDTA-GC surface with Pb{sup 2+} ions was investigated if this electrode could be used as a metal sensor.

Magnetic energy dissipation in force-free jets

Science.gov (United States)

Choudhuri, Arnab Rai; Konigl, Arieh

1986-01-01

It is shown that a magnetic pressure-dominated, supersonic jet which expands or contracts in response to variations in the confining external pressure can dissipate magnetic energy through field-line reconnection as it relaxes to a minimum-energy configuration. In order for a continuous dissipation to occur, the effective reconnection time must be a fraction of the expansion time. The dissipation rate for the axisymmetric minimum-energy field configuration is analytically derived. The results indicate that the field relaxation process could be a viable mechanism for powering the synchrotron emission in extragalactic jets if the reconnection time is substantially shorter than the nominal resistive tearing time in the jet.

Effect of cooling rate on microstructure and deformation behavior of Ti-based metallic glassy/crystalline powders

Energy Technology Data Exchange (ETDEWEB)

Wang, D.J. [State Key Laboratory of Advanced Welding Production Technology, Harbin Institute of Technology, Harbin 150001 (China); School of Mechanical and Mining Engineering, University of Queensland, Brisbane, QLD 4072 (Australia); Huang, Y.J. [State Key Laboratory of Advanced Welding Production Technology, Harbin Institute of Technology, Harbin 150001 (China); Shen, J., E-mail: junshen@hit.edu.cn [State Key Laboratory of Advanced Welding Production Technology, Harbin Institute of Technology, Harbin 150001 (China); Wu, Y.Q.; Huang, H. [School of Mechanical and Mining Engineering, University of Queensland, Brisbane, QLD 4072 (Australia); Zou, J., E-mail: j.zou@uq.edu.au [School of Mechanical and Mining Engineering, University of Queensland, Brisbane, QLD 4072 (Australia); Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD 4072 (Australia)

2010-08-20

The microstructures and deformation behavior of Ti-based metallic powders were comprehensively investigated. It has been found that, with increasing the powder size, the phase constituent alters from pure glassy to glassy with crystalline phases (face centered cubic structured NiSnZr and hexagonal structured Ti{sub 3}Sn phases). Our results suggest that the synergetic effect of the thermodynamics and kinetics determines the subsequent characteristics of the crystalline precipitations. Through comparative nanoindentation tests, it was found that the small powders exhibit more pop-in events and a larger pile-up ratio, suggesting that the plastic deformation of the metallic powders is governed by the combined effects of the free volume and the crystallization, which are determined by the cooling rate.

Understanding Chemical Equilibrium: The Role of Gas Phases and Mixing Contributions in the Minimum of Free Energy Plots

Science.gov (United States)

Tomba, J. Pablo

2017-01-01

The use of free energy plots to understand the concept of thermodynamic equilibrium has been shown to be of great pedagogical value in materials science. Although chemical equilibrium is also amenable to this kind of analysis, it is not part of the agenda of materials science textbooks. Something similar is found in chemistry branches, where free…

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.

The Minimum Binding Energy and Size of Doubly Muonic D3 Molecule

Science.gov (United States)

Eskandari, M. R.; Faghihi, F.; Mahdavi, M.

The minimum energy and size of doubly muonic D3 molecule, which two of the electrons are replaced by the much heavier muons, are calculated by the well-known variational method. The calculations show that the system possesses two minimum positions, one at typically muonic distance and the second at the atomic distance. It is shown that at the muonic distance, the effective charge, zeff is 2.9. We assumed a symmetric planar vibrational model between two minima and an oscillation potential energy is approximated in this region.

Statistical energy as a tool for binning-free, multivariate goodness-of-fit tests, two-sample comparison and unfolding

International Nuclear Information System (INIS)

Aslan, B.; Zech, G.

2005-01-01

We introduce the novel concept of statistical energy as a statistical tool. We define statistical energy of statistical distributions in a similar way as for electric charge distributions. Charges of opposite sign are in a state of minimum energy if they are equally distributed. This property is used to check whether two samples belong to the same parent distribution, to define goodness-of-fit tests and to unfold distributions distorted by measurement. The approach is binning-free and especially powerful in multidimensional applications

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.

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.

Dielectric relaxation and AC conductivity studies of Se90Cd10−xInx glassy alloys

Directory of Open Access Journals (Sweden)

Nitesh Shukla

2016-06-01

Full Text Available Chalcogenide glassy alloys of Se90Cd10−xInx (x = 2, 4, 6, 8 are synthesized by melt quench technique. The prepared glassy alloys have been characterized by techniques such as differential scanning calorimetry (DSC, scanning electron microscopy (SEM and energy dispersive X-ray (EDAX. Dielectric properties of Se90Cd10−xInx (x = 2, 4, 6, 8 chalcogenide glassy system have been studied using impedance spectroscopic technique in the frequency range 42 Hz to 5 MHz at room temperature. It is found that the dielectric constants ɛ′, dielectric loss factor ɛ″ and loss angle Tan δ depend on frequency. ɛ′, ɛ″ and loss angle Tan δ are found to be decreasing with the In content in Se90Cd10−xInx glassy system. AC conductivity of the prepared sample has also been studied. It is found that AC conductivity increases with frequency where as it has decreasing trend with increasing In content in Se–Cd matrix. The semicircles observed in the Cole–Cole plots indicate a single relaxation process.

Evidence for a glassy state in strongly driven carbon

International Nuclear Information System (INIS)

Brown, C.R.D.; Gericke, D.O.; Wunsch, K.; Cammarata, M.; Fritz, D.; Glenzer, S.H.; Heimann, P.; Lee, H.J.; Lemke, H.; Nagler, B.; Zhu, D.; Galtier, E.; Moinard, A.; Rosmej, F.B.

2014-01-01

Here, we report results of an experiment creating a transient, highly correlated carbon state using a combination of optical and x-ray lasers. Scattered x-rays reveal a highly ordered state with an electrostatic energy significantly exceeding the thermal energy of the ions. Strong Coulomb forces are predicted to induce nucleation into a crystalline ion structure within a few picoseconds. However, we observe no evidence of such phase transition after several tens of picoseconds but strong indications for an over-correlated fluid state. The experiment suggests a much slower nucleation and points to an intermediate glassy state where the ions are frozen close to their original positions in the fluid. (authors)

Statistics of energy levels and zero temperature dynamics for deterministic spin models with glassy behaviour

NARCIS (Netherlands)

Degli Esposti, M.; Giardinà, C.; Graffi, S.; Isola, S.

2001-01-01

We consider the zero-temperature dynamics for the infinite-range, non translation invariant one-dimensional spin model introduced by Marinari, Parisi and Ritort to generate glassy behaviour out of a deterministic interaction. It is argued that there can be a large number of metastable (i.e.,

Energy expenditure, economic growth, and the minimum EROI of society

International Nuclear Information System (INIS)

Fizaine, Florian; Court, Victor

2016-01-01

We estimate energy expenditure for the US and world economies from 1850 to 2012. Periods of high energy expenditure relative to GDP (from 1850 to 1945), or spikes (1973–74 and 1978–79) are associated with low economic growth rates, and periods of low or falling energy expenditure are associated with high and rising economic growth rates (e.g. 1945–1973). Over the period 1960–2010 for which we have continuous year-to-year data for control variables (capital formation, population, and unemployment rate) we estimate that, statistically, in order to enjoy positive growth, the US economy cannot afford to spend more than 11% of its GDP on energy. Given the current energy intensity of the US economy, this translates in a minimum societal EROI of approximately 11:1 (or a maximum tolerable average price of energy of twice the current level). Granger tests consistently reveal a one way causality running from the level of energy expenditure (as a fraction of GDP) to economic growth in the US between 1960 and 2010. A coherent economic policy should be founded on improving net energy efficiency. This would yield a “double dividend”: increased societal EROI (through decreased energy intensity of capital investment), and decreased sensitivity to energy price volatility. - Highlights: •We estimate energy expenditures as a fraction of GDP for the US, the world (1850–2012), and the UK (1300–2008). •Statistically speaking, the US economy cannot afford to allocate more than 11% of its GDP to energy expenditures in order to have a positive growth rate. •This corresponds to a maximum tolerable average price of energy of twice the current level. •In the same way, US growth is only possible if its primary energy system has at least a minimum EROI of approximately 11:1.

A path method for finding energy barriers and minimum energy paths in complex micromagnetic systems

International Nuclear Information System (INIS)

Dittrich, R.; Schrefl, T.; Suess, D.; Scholz, W.; Forster, H.; Fidler, J.

2002-01-01

Minimum energy paths and energy barriers are calculated for complex micromagnetic systems. The method is based on the nudged elastic band method and uses finite-element techniques to represent granular structures. The method was found to be robust and fast for both simple test problems as well as for large systems such as patterned granular media. The method is used to estimate the energy barriers in CoCr-based perpendicular recording media

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)

A study of the deep structure of the energy landscape of glassy polystyrene: the exponential distribution of the energy barriers revealed by high-field electron spin resonance spectroscopy

International Nuclear Information System (INIS)

Bercu, V; Martinelli, M; Massa, C A; Pardi, L A; Leporini, D

2004-01-01

The reorientation of one small paramagnetic molecule (spin probe) in glassy polystyrene (PS) is studied by high-field electron spin resonance spectroscopy at two different Larmor frequencies (190 and 285 GHz). The exponential distribution of the energy barriers for the rotational motion of the spin probe is unambiguously evidenced at both 240 and 270 K. The same shape for the distribution of the energy barriers of PS was evidenced by the master curves provided by previous mechanical and light scattering studies. The breadth of the energy barrier distribution of the spin probe is in the range of the estimates of the breadth of the PS energy barrier distribution. The evidence that the deep structure of the energy landscape of PS exhibits the exponential shape of the energy barrier distribution agrees with the results from extreme-value statistics (Bouchaud and Mezard 1997 J. Phys. A: Math. Gen. 30 7997) and the trap model by Bouchaud and co-workers (1996 J. Phys. A: Math. Gen. 29 3847, 2001 Phys. Rev. B 64 104417). (letter to the editor)

Greener energy systems energy production technologies with minimum environmental impact

CERN Document Server

Jeffs, Eric

2012-01-01

Recent years have seen acceleration in the development of cleaner energy systems. In Europe and North America, many old coal-fired power plants will be shut down in the next few years and will likely be replaced by combined cycle plants with higher-efficiency gas turbines that can start up and load quickly. With the revival of nuclear energy, designers are creating smaller nuclear reactors of a simpler integrated design that could expand the application of clean, emission-free energy to industry. And a number of manufacturers now offer hybrid cars with an electric motor and a gasoline engine t

Formation of a glassy phase in ceramic-like coatings

International Nuclear Information System (INIS)

Sazonova, M.V.; Gorbatova, G.N.

1986-01-01

The authors investigate the synthesis directly in coatings of a borosilicate melt that could fill the role of glassy matrix, thereby avoiding fusion and processing of the glassy material. The effect of added boron on the formation of coatings based on molybdenum disilicide and tungsten disilicide in air at 900 degrees C is presented. Without an additive no coating forms; there is no adhesion to the graphite and a continuous film does not form. As a result of boron oxidation an easily fused glassy matrix forms, which bonds the molybdenum disilicide or tungsten disilicide particles together and ensures adhesion to the graphite

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

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

The sorption induced glass transition in amorphous glassy polymers

NARCIS (Netherlands)

van der Vegt, N.F.A.; Wessling, Matthias; Strathmann, H.; Briels, Willem J.

1999-01-01

Sorption of CO2 in both the glassy and the rubbery state of an amorphous polyethylenelike polymer was investigated using molecular dynamics simulations. The temperature was chosen such that the system was in its glassy state at low solute concentrations and its rubbery state at large solute

Dynamical singularities of glassy systems in a quantum quench.

Science.gov (United States)

Obuchi, Tomoyuki; Takahashi, Kazutaka

2012-11-01

We present a prototype of behavior of glassy systems driven by quantum dynamics in a quenching protocol by analyzing the random energy model in a transverse field. We calculate several types of dynamical quantum amplitude and find a freezing transition at some critical time. The behavior is understood by the partition-function zeros in the complex temperature plane. We discuss the properties of the freezing phase as a dynamical chaotic phase, which are contrasted to those of the spin-glass phase in the static system.

The Limit of Free Magnetic Energy in Active Regions

Science.gov (United States)

Moore, Ron; Falconer, David; Sterling, Alphonse

2012-01-01

By measuring from active-region magnetograms a proxy of the free energy in the active region fs magnetic field, it has been found previously that (1) there is an abrupt upper limit to the free energy the field can hold that increases with the amount of magnetic field in the active region, the active region fs magnetic flux content, and (2) the free energy is usually near its limit when the field explodes in a CME/flare eruption. That is, explosive active regions are concentrated in a main-sequence path bordering the free-energy ]limit line in (flux content, free-energy proxy) phase space. Here, from measurement of Marshall Space Flight Center vector magnetograms, we find the magnetic condition that underlies the free ]energy limit and the accompanying main sequence of explosive active regions. Using a suitable free ]energy proxy measured from vector magnetograms of 44 active regions, we find that (1) in active regions at and near their free ]energy limit, the ratio of magnetic-shear free energy to the non ]free magnetic energy the potential field would have is approximately 1 in the core field, the field rooted along the neutral line, and (2) this ratio is progressively less in active regions progressively farther below their free ]energy limit. This shows that most active regions in which this core-field energy ratio is much less than 1 cannot be triggered to explode; as this ratio approaches 1, most active regions become capable of exploding; and when this ratio is 1 or greater, most active regions are compelled to explode. From these results we surmise the magnetic condition that determines the free ]energy limit is the ratio of the free magnetic energy to the non-free energy the active region fs field would have were it completely relaxed to its potential ]field configuration, and that this ratio is approximately 1 at the free-energy limit and in the main sequence of explosive active regions.

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.

Maximum hardness and minimum polarizability principles through lattice energies of ionic compounds

International Nuclear Information System (INIS)

Kaya, Savaş; Kaya, Cemal; Islam, Nazmul

2016-01-01

The maximum hardness (MHP) and minimum polarizability (MPP) principles have been analyzed using the relationship among the lattice energies of ionic compounds with their electronegativities, chemical hardnesses and electrophilicities. Lattice energy, electronegativity, chemical hardness and electrophilicity values of ionic compounds considered in the present study have been calculated using new equations derived by some of the authors in recent years. For 4 simple reactions, the changes of the hardness (Δη), polarizability (Δα) and electrophilicity index (Δω) were calculated. It is shown that the maximum hardness principle is obeyed by all chemical reactions but minimum polarizability principles and minimum electrophilicity principle are not valid for all reactions. We also proposed simple methods to compute the percentage of ionic characters and inter nuclear distances of ionic compounds. Comparative studies with experimental sets of data reveal that the proposed methods of computation of the percentage of ionic characters and inter nuclear distances of ionic compounds are valid.

Maximum hardness and minimum polarizability principles through lattice energies of ionic compounds

Energy Technology Data Exchange (ETDEWEB)

Kaya, Savaş, E-mail: savaskaya@cumhuriyet.edu.tr [Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas 58140 (Turkey); Kaya, Cemal, E-mail: kaya@cumhuriyet.edu.tr [Department of Chemistry, Faculty of Science, Cumhuriyet University, Sivas 58140 (Turkey); Islam, Nazmul, E-mail: nazmul.islam786@gmail.com [Theoretical and Computational Chemistry Research Laboratory, Department of Basic Science and Humanities/Chemistry Techno Global-Balurghat, Balurghat, D. Dinajpur 733103 (India)

2016-03-15

The maximum hardness (MHP) and minimum polarizability (MPP) principles have been analyzed using the relationship among the lattice energies of ionic compounds with their electronegativities, chemical hardnesses and electrophilicities. Lattice energy, electronegativity, chemical hardness and electrophilicity values of ionic compounds considered in the present study have been calculated using new equations derived by some of the authors in recent years. For 4 simple reactions, the changes of the hardness (Δη), polarizability (Δα) and electrophilicity index (Δω) were calculated. It is shown that the maximum hardness principle is obeyed by all chemical reactions but minimum polarizability principles and minimum electrophilicity principle are not valid for all reactions. We also proposed simple methods to compute the percentage of ionic characters and inter nuclear distances of ionic compounds. Comparative studies with experimental sets of data reveal that the proposed methods of computation of the percentage of ionic characters and inter nuclear distances of ionic compounds are valid.

A model for complex flows of soft glassy materials with application to flows through fixed fiber beds

Energy Technology Data Exchange (ETDEWEB)

Sarkar, Arijit; Koch, Donald L., E-mail: dlk15@cornell.edu [School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853-5201 (United States)

2015-11-15

The soft glassy rheology (SGR) model has successfully described the time dependent simple shear rheology of a broad class of complex fluids including foams, concentrated emulsions, colloidal glasses, and solvent-free nanoparticle-organic hybrid materials (NOHMs). The model considers a distribution of mesoscopic fluid elements that hop from trap to trap at a rate which is enhanced by the work done to strain the fluid element. While an SGR fluid has a broad exponential distribution of trap energies, the rheology of NOHMs is better described by a narrower energy distribution and we consider both types of trap energy distributions in this study. We introduce a tensorial version of these models with a hopping rate that depends on the orientation of the element relative to the mean stress field, allowing a range of relative strengths of the extensional and simple shear responses of the fluid. As an application of these models we consider the flow of a soft glassy material through a dilute fixed bed of fibers. The dilute fixed bed exhibits a range of local linear flows which alternate in a chaotic manner with time in a Lagrangian reference frame. It is amenable to an analytical treatment and has been used to characterize the strong flow response of many complex fluids including fiber suspensions, dilute polymer solutions and emulsions. We show that the accumulated strain in the fluid elements has an abrupt nonlinear growth at a Deborah number of order one in a manner similar to that observed for polymer solutions. The exponential dependence of the hopping rate on strain leads to a fluid element deformation that grows logarithmically with Deborah number at high Deborah numbers. SGR fluids having a broad range of trap energies flowing through fixed beds can exhibit a range of rheological behaviors at small Deborah numbers ranging from a yield stress, to a power law response and finally to Newtonian behavior.

A model for complex flows of soft glassy materials with application to flows through fixed fiber beds

KAUST Repository

Sarkar, Arijit

2015-11-01

© 2015 The Society of Rheology. The soft glassy rheology (SGR) model has successfully described the time dependent simple shear rheology of a broad class of complex fluids including foams, concentrated emulsions, colloidal glasses, and solvent-free nanoparticle-organic hybrid materials (NOHMs). The model considers a distribution of mesoscopic fluid elements that hop from trap to trap at a rate which is enhanced by the work done to strain the fluid element. While an SGR fluid has a broad exponential distribution of trap energies, the rheology of NOHMs is better described by a narrower energy distribution and we consider both types of trap energy distributions in this study. We introduce a tensorial version of these models with a hopping rate that depends on the orientation of the element relative to the mean stress field, allowing a range of relative strengths of the extensional and simple shear responses of the fluid. As an application of these models we consider the flow of a soft glassy material through a dilute fixed bed of fibers. The dilute fixed bed exhibits a range of local linear flows which alternate in a chaotic manner with time in a Lagrangian reference frame. It is amenable to an analytical treatment and has been used to characterize the strong flow response of many complex fluids including fiber suspensions, dilute polymer solutions and emulsions. We show that the accumulated strain in the fluid elements has an abrupt nonlinear growth at a Deborah number of order one in a manner similar to that observed for polymer solutions. The exponential dependence of the hopping rate on strain leads to a fluid element deformation that grows logarithmically with Deborah number at high Deborah numbers. SGR fluids having a broad range of trap energies flowing through fixed beds can exhibit a range of rheological behaviors at small Deborah numbers ranging from a yield stress, to a power law response and finally to Newtonian behavior.

A model for complex flows of soft glassy materials with application to flows through fixed fiber beds

KAUST Repository

Sarkar, Arijit; Koch, Donald L.

2015-01-01

© 2015 The Society of Rheology. The soft glassy rheology (SGR) model has successfully described the time dependent simple shear rheology of a broad class of complex fluids including foams, concentrated emulsions, colloidal glasses, and solvent-free nanoparticle-organic hybrid materials (NOHMs). The model considers a distribution of mesoscopic fluid elements that hop from trap to trap at a rate which is enhanced by the work done to strain the fluid element. While an SGR fluid has a broad exponential distribution of trap energies, the rheology of NOHMs is better described by a narrower energy distribution and we consider both types of trap energy distributions in this study. We introduce a tensorial version of these models with a hopping rate that depends on the orientation of the element relative to the mean stress field, allowing a range of relative strengths of the extensional and simple shear responses of the fluid. As an application of these models we consider the flow of a soft glassy material through a dilute fixed bed of fibers. The dilute fixed bed exhibits a range of local linear flows which alternate in a chaotic manner with time in a Lagrangian reference frame. It is amenable to an analytical treatment and has been used to characterize the strong flow response of many complex fluids including fiber suspensions, dilute polymer solutions and emulsions. We show that the accumulated strain in the fluid elements has an abrupt nonlinear growth at a Deborah number of order one in a manner similar to that observed for polymer solutions. The exponential dependence of the hopping rate on strain leads to a fluid element deformation that grows logarithmically with Deborah number at high Deborah numbers. SGR fluids having a broad range of trap energies flowing through fixed beds can exhibit a range of rheological behaviors at small Deborah numbers ranging from a yield stress, to a power law response and finally to Newtonian behavior.

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.

Relationship between energy landscape and low-temperature dynamics of ±J spin glasses

International Nuclear Information System (INIS)

Kobe, S.; Krawczyk, J.

2004-01-01

Clusters and valleys in the exact low-energy landscape of finite Edwards-Anderson ±J spin glasses are related to the distribution of spin domains and free spins in the ground states. The time evolution of the spin correlation function reflects a walk through the landscape at a given temperature and shows typical glassy behaviour

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

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.

Attainability and minimum energy of multiple-stage cascade membrane Systems

KAUST Repository

Alshehri, Ali; Lai, Zhiping

2015-01-01

: View the MathML sourceSn=S1, View the MathML sourceγn=γ1, where n is the number of stages. The minimum energy consumption of a multi-stage membrane process is primarily determined by the membrane selectivity and recycle ratio. A low recycle ratio can

Thermodynamic behavior of glassy state of structurally related compounds.

Science.gov (United States)

Kaushal, Aditya Mohan; Bansal, Arvind Kumar

2008-08-01

Thermodynamic properties of amorphous pharmaceutical forms are responsible for enhanced solubility as well as poor physical stability. The present study was designed to investigate the differences in thermodynamic parameters arising out of disparate molecular structures and associations for four structurally related pharmaceutical compounds--celecoxib, valdecoxib, rofecoxib, and etoricoxib. Conventional and modulated temperature differential scanning calorimetry were employed to study glass forming ability and thermodynamic behavior of the glassy state of model compounds. Glass transition temperature of four glassy compounds was in a close range of 327.6-331.8 K, however, other thermodynamic parameters varied considerably. Kauzmann temperature, strength parameter and fragility parameter showed rofecoxib glass to be most fragile of the four compounds. Glass forming ability of the compounds fared similar in the critical cooling rate experiments, suggesting that different factors were determining the glass forming ability and subsequent behavior of the compounds in glassy state. A comprehensive understanding of such thermodynamic facets of amorphous form would help in rationalizing the approaches towards development of stable glassy pharmaceuticals.

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.

Glassy slag from rotary hearth vitrification

International Nuclear Information System (INIS)

Eschenbach, R.C.; Simpson, M.D.; Paulson, W.S.; Whitworth, C.G.

1995-01-01

Use of a Plasma Arc Centrifugal Treatment (PACT) system for treating mixed wastes containing significant quantities of soil results in formation of a glassy slag which melts at significantly higher temperatures than the borosilicate glasses. The slag typically contains mostly crystalline material, frequently in an amorphous matrix, thus the appellation open-quotes glassy slag.close quotes Details of the PACT process are given. The process will be used for treating buried wastes from Pit 9 at the Idaho National Engineering Laboratory and low-level mixed wastes from nuclear power plants in Switzerland. Properties of the slag after cooling to room temperature are reported, in particular the Product Consistency Test, for a number of different feedstocks. In almost all cases, the results compare favorably with conventional borosilicate glasses. In the PACT system, a transferred arc carries current from the plasma torch to a rotating molten bed of slag, which is the material being heated. Thus this transferred arc adds energy where it is needed - at and near the surface of the molten bath. Material is fed into the furnace through a sealed feeder, and falls into a rotating tub which is heated by the arc. Any organic material is quickly vaporized into the space above the slag bed and burned by the oxygen in the furnace. Metal oxides in the charge are melted into the slag. Metal in the feed tends to melt and collect as a separate phase underneath the slag, but can be oxidized if desired. When oxidized, it unites with other constituents forming a homogeneous slag

The graph-theoretic minimum energy path problem for ionic conduction

Directory of Open Access Journals (Sweden)

Ippei Kishida

2015-10-01

Full Text Available A new computational method was developed to analyze the ionic conduction mechanism in crystals through graph theory. The graph was organized into nodes, which represent the crystal structures modeled by ionic site occupation, and edges, which represent structure transitions via ionic jumps. We proposed a minimum energy path problem, which is similar to the shortest path problem. An effective algorithm to solve the problem was established. Since our method does not use randomized algorithm and time parameters, the computational cost to analyze conduction paths and a migration energy is very low. The power of the method was verified by applying it to α-AgI and the ionic conduction mechanism in α-AgI was revealed. The analysis using single point calculations found the minimum energy path for long-distance ionic conduction, which consists of 12 steps of ionic jumps in a unit cell. From the results, the detailed theoretical migration energy was calculated as 0.11 eV by geometry optimization and nudged elastic band method. Our method can refine candidates for possible jumps in crystals and it can be adapted to other computational methods, such as the nudged elastic band method. We expect that our method will be a powerful tool for analyzing ionic conduction mechanisms, even for large complex crystals.

Glassy Dynamics

DEFF Research Database (Denmark)

Jensen, Henrik J.; Sibani, Paolo

2007-01-01

The term glassy dynamics is often used to refer to the extremely slow relaxation observed in several types of many component systems. The time span needed to reach a steady, time independent, state will typically be far beyond experimentally accessible time scales. When melted alloys are cooled...... down they typically do not enter a crystalline ordered state. Instead the atoms retain the amorphous arrangement characteristic of the liquid high temperature phase while the mobility of the molecules decreases very many orders of magnitude. This colossal change in the characteristic dynamical time...

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.

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.

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.

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.

Atmospheric pressure plasma treatment of glassy carbon for adhesion improvement

DEFF Research Database (Denmark)

Kusano, Yukihiro; Mortensen, Henrik Junge; Stenum, Bjarne

2007-01-01

density increased with the plasma treatments. Adhesion test of the treated glassy carbon covered with cured epoxy showed cohesive failure, indicating strong bonding after the treatments. This is in contrast to the adhesion tests of untreated samples where the epoxy readily peeled off the glassy carbon....

Projected electricity savings from implementing minimum energy efficiency standard for household refrigerators in Malaysia

International Nuclear Information System (INIS)

Mahlia, T.M.I.; Masjuki, H.H.; Saidur, R.; Choudhury, I.A.; NoorLeha, A.R.

2003-01-01

The Malaysian economy has grown rapidly in the last two decades. This growth has increased the ownership of household electrical appliances, especially refrigerator-freezers. Almost every house in Malaysia owns a refrigerator-freezer. The Malaysia Energy Center considered implementing a minimum energy efficiency standard for household refrigerator-freezers sometime in the coming year. This paper attempts to predict the amount of energy savings in the residential sector by implementing a minimum energy efficiency standard for household refrigerator-freezers. The calculations are based on the growth of refrigerator-freezer ownership data in Malaysian households. By implementing the programs in 2004, about 8722 GWh will be saved in the year 2013. Therefore, efficiency improvement of this appliance will provide a significant impact in future electricity consumption in Malaysia

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…

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.

Globally optimal, minimum stored energy, double-doughnut superconducting magnets.

Science.gov (United States)

Tieng, Quang M; Vegh, Viktor; Brereton, Ian M

2010-01-01

The use of the minimum stored energy current density map-based methodology of designing closed-bore symmetric superconducting magnets was described recently. The technique is further developed to cater for the design of interventional-type MRI systems, and in particular open symmetric magnets of the double-doughnut configuration. This extends the work to multiple magnet domain configurations. The use of double-doughnut magnets in MRI scanners has previously been hindered by the ability to deliver strong magnetic fields over a sufficiently large volume appropriate for imaging, essentially limiting spatial resolution, signal-to-noise ratio, and field of view. The requirement of dedicated interventional space restricts the manner in which the coils can be arranged and placed. The minimum stored energy optimal coil arrangement ensures that the field strength is maximized over a specific region of imaging. The design method yields open, dual-domain magnets capable of delivering greater field strengths than those used prior to this work, and at the same time it provides an increase in the field-of-view volume. Simulation results are provided for 1-T double-doughnut magnets with at least a 50-cm 1-ppm (parts per million) field of view and 0.7-m gap between the two doughnuts. Copyright (c) 2009 Wiley-Liss, Inc.

Materializing a responsive interior: designing minimum energy structures

DEFF Research Database (Denmark)

Mossé, Aurélie; Kofod, Guggi; Ramsgaard Thomsen, Mette

2011-01-01

This paper discusses a series of design-led experiments investigating future possibilities for architectural materialization relying on minimum energy structures as an example of adaptive structure. The structures have been made as laminates of elastic membrane under high tension with flexible...... (Lendlein, Kelch 2002) or light (van Oosten, Bastiaansen et al. 2009). All in all, this approach could form a whole new design paradigm, in which efficient 2D-manufacturing can lead to highly flexible, low weight and adaptable 3D-structures. This is illustrated by the design and manufacture of electro...

Quasi-equilibrium in glassy dynamics: an algebraic view

International Nuclear Information System (INIS)

Franz, Silvio; Parisi, Giorgio

2013-01-01

We study a chain of identical glassy systems in a constrained equilibrium, where each bond of the chain is forced to remain at a preassigned distance to the previous one. We apply this description to mean-field glassy systems in the limit of a long chain where each bond is close to the previous one. We show that this construction defines a pseudo-dynamic process that in specific conditions can formally describe real relaxational dynamics for long times. In particular, in mean-field spin glass models we can recover in this way the equations of Langevin dynamics in the long time limit at the dynamical transition temperature and below. We interpret the formal identity as evidence that in these situations the configuration space is explored in a quasi-equilibrium fashion. Our general formalism, which relates dynamics to equilibrium, puts slow dynamics in a new perspective and opens the way to the computation of new dynamical quantities in glassy systems. (paper)

Free-Energy Barrier of Filling a Spherical Cavity in the Presence of Line Tension: Implication to the Energy Barrier between the Cassie and Wenzel States on a Superhydrophobic Surface with Spherical Cavities.

Science.gov (United States)

Iwamatsu, Masao

2016-09-20

The free-energy barrier of filling a spherical cavity having an inner wall of various wettabilities is studied. The morphology and free energy of a lens-shaped droplet are determined from the minimum of the free energy. The effect of line tension on the free energy is also studied. Then, the equilibrium contact angle of the droplet is determined from the generalized Young's equation. By increasing the droplet volume within the spherical cavity, the droplet morphology changes from spherical with an equilibrium contact angle of 180° to a lens with a convex meniscus, where the morphological complete drying transition occurs. By further increasing the droplet volume, the meniscus changes from convex to concave. Then, the lens-shaped droplet with concave meniscus spreads over the whole inner wall, resulting in an equilibrium contact angle of 0° to leave a spherical bubble, where the morphological complete wetting transition occurs. Finally, the whole cavity is filled with liquid. The free energy shows a barrier from complete drying to complete wetting as a function of droplet volume, which corresponds to the energy barrier between the Cassie and Wenzel states of the superhydrophobic surface with spherical cavities. The free-energy maximum occurs when the meniscus of the droplet becomes flat, and it is given by an analytic formula. The effect of line tension is expressed by the scaled line tension, and this effect is largest at the free-energy maximum. The positive line tension increases the free-energy maximum, which thus increases the stability of the Cassie superhydrophobic state, whereas the negative line tension destabilizes the superhydrophobic state.

Aryl Diazonium Chemistry for the Surface Functionalization of Glassy Biosensors.

Science.gov (United States)

Zheng, Wei; van den Hurk, Remko; Cao, Yong; Du, Rongbing; Sun, Xuejun; Wang, Yiyu; McDermott, Mark T; Evoy, Stephane

2016-03-14

Nanostring resonator and fiber-optics-based biosensors are of interest as they offer high sensitivity, real-time measurements and the ability to integrate with electronics. However, these devices are somewhat impaired by issues related to surface modification. Both nanostring resonators and photonic sensors employ glassy materials, which are incompatible with electrochemistry. A surface chemistry approach providing strong and stable adhesion to glassy surfaces is thus required. In this work, a diazonium salt induced aryl film grafting process is employed to modify a novel SiCN glassy material. Sandwich rabbit IgG binding assays are performed on the diazonium treated SiCN surfaces. Fluorescently labelled anti-rabbit IgG and anti-rabbit IgG conjugated gold nanoparticles were used as markers to demonstrate the absorption of anti-rabbit IgG and therefore verify the successful grafting of the aryl film. The results of the experiments support the effectiveness of diazonium chemistry for the surface functionalization of SiCN surfaces. This method is applicable to other types of glassy materials and potentially can be expanded to various nanomechanical and optical biosensors.

Aryl Diazonium Chemistry for the Surface Functionalization of Glassy Biosensors

Directory of Open Access Journals (Sweden)

Wei Zheng

2016-03-01

Full Text Available Nanostring resonator and fiber-optics-based biosensors are of interest as they offer high sensitivity, real-time measurements and the ability to integrate with electronics. However, these devices are somewhat impaired by issues related to surface modification. Both nanostring resonators and photonic sensors employ glassy materials, which are incompatible with electrochemistry. A surface chemistry approach providing strong and stable adhesion to glassy surfaces is thus required. In this work, a diazonium salt induced aryl film grafting process is employed to modify a novel SiCN glassy material. Sandwich rabbit IgG binding assays are performed on the diazonium treated SiCN surfaces. Fluorescently labelled anti-rabbit IgG and anti-rabbit IgG conjugated gold nanoparticles were used as markers to demonstrate the absorption of anti-rabbit IgG and therefore verify the successful grafting of the aryl film. The results of the experiments support the effectiveness of diazonium chemistry for the surface functionalization of SiCN surfaces. This method is applicable to other types of glassy materials and potentially can be expanded to various nanomechanical and optical biosensors.

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.

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.

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.

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.

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)

Dielectric relaxation studies in super-cooled liquid and glassy phases of anti-cancerous alkaloid: Brucine

Science.gov (United States)

Afzal, Aboothahir; Shahin Thayyil, M.; Sulaiman, M. K.; Kulkarni, A. R.

2018-05-01

Brucine has good anti-tumor effects, on both liver cancer and breast cancer. It has bioavailability of 40.83%. Since the bioavailability of the drug is low, an alternative method to increase its bioavailability and solubility is by changing the drug into glassy form. We used Differential Scanning Calorimetry (DSC) for studying the glass forming ability of the drug. Brucine was found to be a very good glass former glass transition temperature 365 K. Based on the DSC analysis we have used broadband dielectric spectroscopy (BDS) for studying the drug in the super cooled and glassy state. BDS is an effective tool to probe the molecular dynamics in the super cooled and glassy state. Molecular mobility is found to be present even in the glassy state of this active pharmaceutical ingredient (API) which is responsible for the instability. Our aim is to study the factors responsible for instability of this API in amorphous form. Cooling curves for dielectric permittivity and dielectric loss revealed the presence of structural (α) and secondary relaxations (β and γ). Temperature dependence of relaxation time is fitted by Vogel-Fulcher-Tammann equation and found the values of activation energy of the α relaxation, fragility and glass transition temperature. Paluch's anti correlation is also verified, that the width of the α-loss peak at or near the glass transition temperature Tg is strongly anticorrelated with the polarity of the molecule. The larger the dielectric relaxation strength Δɛ (Tg) of the system, the narrower is the α-loss peak (higher value of βKWW).

Deformed special relativity with an energy barrier of a minimum speed

International Nuclear Information System (INIS)

Nassif, Claudio

2011-01-01

Full text: This research aims to introduce a new principle of symmetry in the flat space-time by means of the elimination of the classical idea of rest, and by including a universal minimum limit of speed in the quantum world. Such a limit, unattainable by the particles, represents a preferred inertial reference frame associated with a universal background field that breaks Lorentz symmetry. So there emerges a new relativistic dynamics where a minimum speed forms an inferior energy barrier. One of the interesting implications of the existence of such a minimum speed is that it prevents the absolute zero temperature for an ultracold gas, according to the third law of thermodynamics. So we will be able to provide a fundamental dynamical explanation for the third law by means of a connection between such a phenomenological law and the new relativistic dynamics with a minimum speed. In other words we say that our relevant investigation is with respect to the problem of the absolute zero temperature in the thermodynamics of an ideal gas. We have made a connection between the 3 rd law of Thermodynamics and the new dynamics with a minimum speed by means of a relation between the absolute zero temperature (T = 0 deg K) and a minimum average speed (V) for a gas with N particles (molecules or atoms). Since T = 0 deg K is thermodynamically unattainable, we have shown this is due to the impossibility of reaching V from the new dynamics standpoint. (author)

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

processes occurring at constant temperatures and volumes. In physics, the minimum free energy corresponds to an equilibrium state to which an isochoric-isothermal system relaxes [4,5]. It is obvious that the biological systems considered by the authors are fundamentally non-equilibrium, do not seek equilibrium, and, in most cases, do not retain their volumes as they develop. For a biological system, the equilibrium means death, decay. Therefore, to base the idea of life on FEP is the same as to state that the pursuit of death is the purpose and meaning of life. In order to consider processes addressed by the authors, one needs functionals employed in non-equilibrium rather than equilibrium thermodynamics [6-8]. Specifically, I would like to draw their attention to the rate of change of the Gibbs energy with time, or entropy production (the maximum entropy production principle can be useful here [7,9-12]).

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.

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.

Energy buildup in sheared force-free magnetic fields

Science.gov (United States)

Wolfson, Richard; Low, Boon C.

1992-01-01

Photospheric displacement of the footpoints of solar magnetic field lines results in shearing and twisting of the field, and consequently in the buildup of electric currents and magnetic free energy in the corona. The sudden release of this free energy may be the origin of eruptive events like coronal mass ejections, prominence eruptions, and flares. An important question is whether such an energy release may be accompanied by the opening of magnetic field lines that were previously closed, for such open field lines can provide a route for matter frozen into the field to escape the sun altogether. This paper presents the results of numerical calculations showing that opening of the magnetic field is permitted energetically, in that it is possible to build up more free energy in a sheared, closed, force-free magnetic field than is in a related magnetic configuration having both closed and open field lines. Whether or not the closed force-free field attains enough energy to become partially open depends on the form of the shear profile; the results presented compare the energy buildup for different shear profiles. Implications for solar activity are discussed briefly.

Pressure-induced transformations in computer simulations of glassy water

Science.gov (United States)

Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas

2013-11-01

Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a "P-T phase diagram" for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water.

Electrochemical and microstructural characterization of platinum supported on glassy carbon

Directory of Open Access Journals (Sweden)

Terzić Sanja

2007-01-01

Full Text Available The effect of the electrochemical oxidation of glassy carbon on the deposition of platinum particles and the electrocatalytic activity of platinum supported on oxidized glassy carbon were studied for methanol oxidation in H2SO4 solution. Platinum was potentiostatically deposited from H2SO4 + 6mM H2PtCl6 solution. Glassy carbon was anodically polarized in 1 M NaOH at 1.41 V (SCE for 35 and 95 s and in 0.5 M H2SO4 at 2V (SCE for 35; 95 s and 2.25 V for 35 and 95 s. Electrochemical treatment of the GC support leads to a better distribution of platinum on the substrate and has remarkable effect on the activity. The activity of the Pt/GCox electrode for methanol oxidation is larger than that of polycrystalline Pt and by more than one order of magnitude larger than that of a Pt/GC electrode. This increase in activity indicates the pronounced role of the organic residues of the GC support on the properties of Pt particles deposited on glassy carbon.

On the solubility advantage of a pharmaceutical’s glassy state over the crystal state, and of its crystal polymorphs

International Nuclear Information System (INIS)

Johari, G.P.; Shanker, Ravi M.

2014-01-01

Highlights: • Heat capacity data do not yield the solubility advantage of amorphous and metastable crystal pharmaceuticals. • There is no reversible equilibrium of an amorphous solid with its saturated solution. • Solubility advantage of an amorphous solid depends upon the solvent and other interactions. - Abstract: At equilibrium, the saturation solubility and vapor pressure of a material in a state of high free energy are greater than in its state of low free energy. This knowledge from classical thermodynamics is currently used for increasing the solubility of crystalline pharmaceuticals by producing them in their glassy state, or in other solid states of high free energy. The ratio of the apparent saturation solubility of these solids to that of a crystal, calculated from the thermodynamic data of the pure solute, ϕ cal , is called the solubility advantage, and it is used as a guide for increasing the solubility of a pharmaceutical. We argue that the ϕ cal differs from the measured solubility ratio, ϕ meas , because, (i) ϕ cal is independent of the solvent, but ϕ meas is not so, (ii) ϕ cal would increase with the dissolution time monotonically to a constant value, but ϕ meas would first reach a maximum and then decrease, and (iii) approximations are made in estimating ϕ cal and the effect of thermal history on high free energy solids is ignored. On the other hand, ϕ meas is affected by, (a) another chemical equilibrium in the solution, e.g., hydrogen-bond formation and ionic dissociation, (b) the production method and thermal history of a glass or an amorphous samples, and (c) mutarotation in the solution, isomerization or tautomeric conversion in the solid. We also discuss the effects of structural relaxation and crystallization on ϕ meas . The ϕ meas value of a (crystal) polymorph would be affected by all the three, and further if the polymorph is orientationally disordered. We provide evidence for these effects from analysis of the known

Completely boundary-free minimum and maximum principles for neutron transport and their least-squares and Galerkin equivalents

International Nuclear Information System (INIS)

Ackroyd, R.T.

1982-01-01

Some minimum and maximum variational principles for even-parity neutron transport are reviewed and the corresponding principles for odd-parity transport are derived by a simple method to show why the essential boundary conditions associated with these maximum principles have to be imposed. The method also shows why both the essential and some of the natural boundary conditions associated with these minimum principles have to be imposed. These imposed boundary conditions for trial functions in the variational principles limit the choice of the finite element used to represent trial functions. The reasons for the boundary conditions imposed on the principles for even- and odd-parity transport point the way to a treatment of composite neutron transport, for which completely boundary-free maximum and minimum principles are derived from a functional identity. In general a trial function is used for each parity in the composite neutron transport, but this can be reduced to one without any boundary conditions having to be imposed. (author)

CONCEPT OF THE MINIMUM ENERGY PASSENGER CAR WITH USE OF UNCONVENTIONAL ENERGY SOURCES

Directory of Open Access Journals (Sweden)

V. A. Gabrinets

2014-06-01

Full Text Available Purpose. The paper is aimed to consider the concept of creation of the minimum energy passenger car with use of nonconventional energy sources and the walls that have enhanced thermal insulation properties. Мethodology. The types of heat losses, as well as their value were analyzed. The alternative sources of energy are considered for heating. Their potential contribution to the overall energy balance of the passenger car is analyzed. Impact on the car design of the enhanced wall thermal insulation, solar energy inflow through the transparent windows and energy release of passengers are quantitatively evaluated. Findings. With the maximum possible use of all unconventional energy sources and the rational scheme solutions of conditioning and heating systems energy the costs for these needs for a passenger car can be reduced by 40-50%. Originality. New types of energy to maintain the heat balance of the car in the winter period is proposed to use firstly. New schematics solutions for environmental control system of the car both in winter and in summer periods were offered. Practical value. Introduction of the proposed scheme solutions and approaches to ensure the comfortable conditions for passengers may be implemented on an existing park of passenger cars and do not require a major re-equipment of systems that have already been installed.

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.

Electrocatalytic performance of Pu(IV)/Pu(III) redox reaction at graphene modified glassy carbon electrode

International Nuclear Information System (INIS)

Gupta, Ruma; Gamare, J.S.; Kamat, J.V.; Aggarwal, S.K.

2014-01-01

In this paper we explore the analytical perspectives of graphene modified electrode utilising commercially available graphene, which is well characterised, completely free from surfactants and has not been purposely oxidised or treated. We compare and critically contrast the electro-analytical performance of graphene modified glassy carbon electrodes (Gr/GC) with that of unmodified GC electrode towards Pu(IV)/Pu(III) redox reaction, monitoring of which has considerable importance in a plethora of areas where electrochemistry is conveniently and beneficially utilised for determination of nuclear fuels

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

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...

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

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.

A novel lable-free electrochemical immunosensor for carcinoembryonic antigen based on gold nanoparticles-thionine-reduced graphene oxide nanocomposite film modified glassy carbon electrode.

Science.gov (United States)

Kong, Fen-Ying; Xu, Mao-Tian; Xu, Jing-Juan; Chen, Hong-Yuan

2011-10-15

In this paper, gold nanoparticle-thionine-reduced graphene oxide (GNP-THi-GR) nanocomposites were prepared to design a label-free immunosensor for the sensitive detection of carcinoembryonic antigen (CEA). The nanocomposites with good biocompatibility, excellent redox electrochemical activity and large surface area were coated onto the glassy carbon electrode (GCE) surface and then CEA antibody (anti-CEA) was immobilized on the electrode to construct the immunosensor. The morphologies and electrochemistry of the formed nanocomposites were investigated by using scanning electron microscopy (SEM), ultraviolet-visible (UV-vis) spectrometry, electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). CV and differential pulse voltammetry (DPV) studies demonstrated that the formation of antibody-antigen complexes decreased the peak current of THi in the GNP-THi-GR nanocomposites. The decreased currents were proportional to the CEA concentration in the range of 10-500 pg/mL with a detection limit of 4 pg/mL. The proposed method was simple, fast and inexpensive for the determination of CEA at very low levels. Copyright © 2011 Elsevier B.V. All rights reserved.

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

Dynamics and Geometry of Icosahedral Order in Liquid and Glassy Phases of Metallic Glasses

Directory of Open Access Journals (Sweden)

Masato Shimono

2015-07-01

Full Text Available The geometrical properties of the icosahedral ordered structure formed in liquid and glassy phases of metallic glasses are investigated by using molecular dynamics simulations. We investigate the Zr-Cu alloy system as well as a simple model for binary alloys, in which we can change the atomic size ratio between alloying components. In both cases, we found the same nature of icosahedral order in liquid and glassy phases. The icosahedral clusters are observed in liquid phases as well as in glassy phases. As the temperature approaches to the glass transition point Tg, the density of the clusters rapidly grows and the icosahedral clusters begin to connect to each other and form a medium-range network structure. By investigating the geometry of connection between clusters in the icosahedral network, we found that the dominant connecting pattern is the one sharing seven atoms which forms a pentagonal bicap with five-fold symmetry. From a geometrical point of view, we can understand the mechanism of the formation and growth of the icosahedral order by using the Regge calculus, which is originally employed to formulate a theory of gravity. The Regge calculus tells us that the distortion energy of the pentagonal bicap could be decreased by introducing an atomic size difference between alloying elements and that the icosahedral network would be stabilized by a considerably large atomic size difference.

Gold nanoparticle/multi-walled carbon nanotube modified glassy carbon electrode as a sensitive voltammetric sensor for the determination of diclofenac sodium.

Science.gov (United States)

Afkhami, Abbas; Bahiraei, Atousa; Madrakian, Tayyebeh

2016-02-01

A simple and highly sensitive sensor for the determination of diclofenac sodium based on gold nanoparticle/multi-walled carbon nanotube modified glassy carbon electrode is reported. Scanning electron microscopy along with energy dispersive X-ray spectroscopy, electrochemical impedance spectroscopy, cyclic voltammetry and square wave voltammetry was used to characterize the nanostructure and performance of the sensor and the results were compared with those obtained at the multi-walled carbon nanotube modified glassy carbon electrode and bare glassy carbon electrode. Under the optimized experimental conditions diclofenac sodium gave linear response over the range of 0.03-200μmolL(-1). The lower detection limits were found to be 0.02μmolL(-1). The effect of common interferences on the current response of DS was investigated. The practical application of the modified electrode was demonstrated by measuring the concentration of diclofenac sodium in urine and pharmaceutical samples. This revealed that the gold nanoparticle/multiwalled carbon nanotube modified glassy carbon electrode shows excellent analytical performance for the determination of diclofenac sodium in terms of a very low detection limit, high sensitivity, very good accuracy, repeatability and reproducibility. Copyright © 2015 Elsevier B.V. All rights reserved.

Electrical studies on silver based fast ion conducting glassy materials

International Nuclear Information System (INIS)

Rao, B. Appa; Kumar, E. Ramesh; Kumari, K. Rajani; Bhikshamaiah, G.

2014-01-01

Among all the available fast ion conductors, silver based glasses exhibit high conductivity. Further, glasses containing silver iodide enhances fast ion conducting behavior at room temperature. Glasses of various compositions of silver based fast ion conductors in the AgI−Ag 2 O−[(1−x)B 2 O 3 −xTeO 2 ] (x=0 to1 mol% in steps of 0.2) glassy system have been prepared by melt quenching method. The glassy nature of the compounds has been confirmed by X-ray diffraction. The electrical conductivity (AC) measurements have been carried out in the frequency range of 1 KHz–3MHz by Impedance Analyzer in the temperature range 303–423K. The DC conductivity measurements were also carried out in the temperature range 300–523K. From both AC and DC conductivity studies, it is found that the conductivity increases and activation energy decreases with increasing the concentration of TeO 2 as well as with temperature. The conductivity of the present glass system is found to be of the order of 10 −2 S/cm at room temperature. The ionic transport number of these glasses is found to be 0.999 indicating that these glasses can be used as electrolyte in batteries

Thermodynamical modeling of nuclear glasses: coexistence of amorphous phases

International Nuclear Information System (INIS)

Adjanor, G.

2007-11-01

Investigating the stability of borosilicate glasses used in the nuclear industry with respect to phase separation requires to estimate the Gibbs free energies of the various phases appearing in the material. In simulation, using current computational resources, a direct state-sampling of a glassy system with respect to its ensemble statistics is not ergodic and the estimated ensemble averages are not reliable. Our approach consists in generating, at a given cooling rate, a series of quenches, or paths connecting states of the liquid to states of the glass, and then in taking into account the probability to generate the paths leading to the different glassy states in ensembles averages. In this way, we introduce a path ensemble formalism and calculate a Landau free energy associated to a glassy meta-basin. This method was validated by accurately mapping the free energy landscape of a 38-atom glassy cluster. We then applied this approach to the calculation of the Gibbs free energies of binary amorphous Lennard-Jones alloys, and checked the correlation between the observed tendencies to order or to phase separate and the computed Gibbs free energies. We finally computed the driving force to phase separation in a simplified three-oxide nuclear glass modeled by a Born-Mayer-Huggins potential that includes a three-body term, and we compared the estimated quantities to the available experimental data. (author)

Thermodynamical modeling of nuclear glasses: coexistence of amorphous phases; Modelisation thermodynamique des verres nucleaires: coexistence entre phases amorphes

Energy Technology Data Exchange (ETDEWEB)

Adjanor, G

2007-11-15

Investigating the stability of borosilicate glasses used in the nuclear industry with respect to phase separation requires to estimate the Gibbs free energies of the various phases appearing in the material. In simulation, using current computational resources, a direct state-sampling of a glassy system with respect to its ensemble statistics is not ergodic and the estimated ensemble averages are not reliable. Our approach consists in generating, at a given cooling rate, a series of quenches, or paths connecting states of the liquid to states of the glass, and then in taking into account the probability to generate the paths leading to the different glassy states in ensembles averages. In this way, we introduce a path ensemble formalism and calculate a Landau free energy associated to a glassy meta-basin. This method was validated by accurately mapping the free energy landscape of a 38-atom glassy cluster. We then applied this approach to the calculation of the Gibbs free energies of binary amorphous Lennard-Jones alloys, and checked the correlation between the observed tendencies to order or to phase separate and the computed Gibbs free energies. We finally computed the driving force to phase separation in a simplified three-oxide nuclear glass modeled by a Born-Mayer-Huggins potential that includes a three-body term, and we compared the estimated quantities to the available experimental data. (author)

Electrical properties of carbon nanotubes modified GaSe glassy system

Science.gov (United States)

Khan, Hana; Khan, Zubair M. S. H.; Islam, Shama; Rahman, Raja Saifu; Husain, M.; Zulfequar, M.

2018-05-01

In this paper we report the investigation of the effect of Carbon Nanotubes (CNT) addition on the electrical properties of GaSe Glassy system. Dielectric constant and dielectric loss of GaSe glassy system are found to increase on CNT addition. The conductivity of GaSe glasy systems is also found to increase on CNT addition. This behavior is attributed to the excellent conduction properties of Carbon Nanotube.

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.

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.

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

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.

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.

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

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.

Thermonuclear reactor materials composed of glassy carbons

International Nuclear Information System (INIS)

Kazumata, Yukio.

1979-01-01

Purpose: To improve the durability to plasma radiation by the use of glassy carbon as the structural materials for the first wall and the blanket in thermonuclear devices. Constitution: The glassy carbon (glass-like carbon) is obtained by forming specific organic substances into a predetermined configuration and carbonizing them by heat decomposition under special conditions. They are impermeable carbon material of 1.40 - 1.70 specific gravity, less graphitizable and being almost in isotropic crystal forms in which isotropic structure such as in graphite is scarcely observed. They have an extremely high hardness, are less likely to be damaged when exposed to radiation and have great strength and corrosion resistance. Accordingly, the service life of the reactor walls and the likes can remarkably be increased by using the materials. (Horiuchi, T.)

Minimum spanning trees and random resistor networks in d dimensions.

Science.gov (United States)

Read, N

2005-09-01

We consider minimum-cost spanning trees, both in lattice and Euclidean models, in d dimensions. For the cost of the optimum tree in a box of size L , we show that there is a correction of order L(theta) , where theta or =1 . The arguments all rely on the close relation of Kruskal's greedy algorithm for the minimum spanning tree, percolation, and (for some arguments) random resistor networks. The scaling of the entropy and free energy at small nonzero T , and hence of the number of near-optimal solutions, is also discussed. We suggest that the Steiner tree problem is in the same universality class as the minimum spanning tree in all dimensions, as is the traveling salesman problem in two dimensions. Hence all will have the same value of theta=-3/4 in two dimensions.

Glassy aerosols with a range of compositions nucleate ice heterogeneously at cirrus temperatures

Directory of Open Access Journals (Sweden)

T. W. Wilson

2012-09-01

Full Text Available Atmospheric secondary organic aerosol (SOA is likely to exist in a semi-solid or glassy state, particularly at low temperatures and humidities. Previously, it has been shown that glassy aqueous citric acid aerosol is able to nucleate ice heterogeneously under conditions relevant to cirrus in the tropical tropopause layer (TTL. In this study we test if glassy aerosol distributions with a range of chemical compositions heterogeneously nucleate ice under cirrus conditions. Three single component aqueous solution aerosols (raffinose, 4-hydroxy-3-methoxy-DL-mandelic acid (HMMA and levoglucosan and one multi component aqueous solution aerosol (raffinose mixed with five dicarboxylic acids and ammonium sulphate were studied in both the liquid and glassy states at a large cloud simulation chamber. The investigated organic compounds have similar functionality to oxidised organic material found in atmospheric aerosol and have estimated temperature/humidity induced glass transition thresholds that fall within the range predicted for atmospheric SOA. A small fraction of aerosol particles of all compositions were found to nucleate ice heterogeneously in the deposition mode at temperatures relevant to the TTL (<200 K. Raffinose and HMMA, which form glasses at higher temperatures, nucleated ice heterogeneously at temperatures as high as 214.6 and 218.5 K respectively. We present the calculated ice active surface site density, n_s, of the aerosols tested here and also of glassy citric acid aerosol as a function of relative humidity with respect to ice (RH_i. We also propose a parameterisation which can be used to estimate heterogeneous ice nucleation by glassy aerosol for use in cirrus cloud models up to ~220 K. Finally, we show that heterogeneous nucleation by glassy aerosol may compete with ice nucleation on mineral dust particles in mid-latitudes cirrus.

Positron annihilation study of graphite, glassy carbon and C60/C70 fullerene

International Nuclear Information System (INIS)

Hasegawa, Masayuki; Kajino, Masahiro; Yamaguchi, Sadae; Iwata, Tadao; Kuramoto, Eiichi; Takenaka, Minoru.

1992-01-01

ACAR (Angular Correlation of Annihilation Radiation) and positron lifetime measurements have been made on, HOPG (Highly Oriented Pyrolytic Graphite), isotropic fine-grained graphite, glassy carbons and C 60 /C 70 powder. HOPG showed marked bimodality along the c-axis and anisotropy in ACAR momentum distribution, which stem from characteristic annihilation between 'interlayer' positrons and π-electrons in graphite. ACAR curves of the isotropic graphite and glassy carbons are even narrower than that of HOPG perpendicular to the c-axis. Positron lifetime of 420 and 390 - 480 psec, much longer than that of 221 psec in HOPG, were observed for the isotropic graphite and glassy carbons respectively, which are due to positron trapping in structural voids in them. Positron lifetime and ACAR width (FWHM) can be well correlated to void sizes (1.7 to 5.0 nm) of glassy carbons which have been determined by small angle neutron (SAN) scattering measurements. ACAR curves and positron lifetime of C 60 /C 70 powder agree well with those of glassy carbons. This shows that positron wave functions extend, as in the voids of glassy carbons, much wider than open spaces of the octahedral interstices of the face-centered cubic (FCC) structure of C 60 crystal and strongly suggests positron trapping in the 'soccer ball' vacancy. Possible positron states in the carbon materials are discussed with a simple model of void volume-trapping. Preliminary results on neutron irradiation damage in HOPG are also presented. (author)

Thin film plasma coatings from dielectric free-flowing materials

International Nuclear Information System (INIS)

Timofeeva, L.A.; Katrich, S.A.; Solntsev, L.A.

1994-01-01

Fabrication of thin film plasma coatings from insulating free-flowing materials is considered. Molybdenum-tart ammonium coating of 3...5 μ thickness deposited on glassy carbon, aluminium, silicon, nickel, cast iron and steel substrates in 'Bulat-ZT' machine using insulating free-flowing materials cathod was found to form due to adsorption, absorption and dissuasion processes. The use of insulating free-flowing materials coatings allow to exclude pure metals cathods in plasma-plating process

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.

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.)

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.)

Using low-field NMR to infer the physical properties of glassy oligosaccharide/water mixtures.

Science.gov (United States)

Aeberhardt, Kasia; Bui, Quang D; Normand, Valéry

2007-03-01

Low-field NMR (LF-NMR) is usually used as an analytical technique, for instance, to determine water and oil contents. For this application, no attempt is made to understand the physical origin of the data. Here we build a physical model to explain the five fit parameters of the conventional free induction decay (FID) for glassy oligosaccharide/water mixtures. The amplitudes of the signals from low-mobility and high-mobility protons correspond to the density of oligosaccharide protons and water protons, respectively. The relaxation time of the high-mobility protons is described using a statistical model for the probability that oligosaccharide hydroxyl groups form multiple hydrogen bonds. The variation of energy of the hydrogen bond is calculated from the average bond distance and the average angle contribution. Applying the model to experimental data shows that hydrogen atoms screen the water oxygen atoms when two water molecules solvate a single hydroxyl group. Furthermore, the relaxation time of the oligosaccharide protons is independent of its molecular weight and the water content. Finally, inversion of the FID using the inverse Laplace transform gives the continuous spectrum of relaxation times, which is a fingerprint of the oligosaccharide.

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.

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

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

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.

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.)

Voltammetric quantitation of nitazoxanide by glassy carbon electrode

Directory of Open Access Journals (Sweden)

Rajeev Jain

2013-12-01

Full Text Available The present study reports voltammetric reduction of nitazoxanide in Britton–Robinson (B–R buffer by cyclic and square-wave voltammetry at glassy carbon electrode. A versatile fully validated voltammetric method for quantitative determination of nitazoxanide in pharmaceutical formulation has been proposed. A squrewave peak current was linear over the nitazoxanide concentration in the range of 20–140 µg/mL. The limit of detection (LOD and limit of quantification (LOQ was calculated to be 5.23 μg/mL and 17.45 μg/mL, respectively. Keywords: Nitazoxanide, Squarewave voltammetry, Glassy carbon electrode, Pharmaceutical formulation

New model system in radiation cryochemistry. Hyperquenched glassy water

International Nuclear Information System (INIS)

Plonka, A.

1998-01-01

Complete text of publication follows. Since the radical generated by high-energy irradiation of liquid water are short-lived at ambient temperature, they are often studied at cryogenic temperatures after irradiating either crystalline ice or highly concentrated aqueous electrolyte solution glasses. While these studies provided a wealth of information, they also bear disadvantages in that further reactions of these radicals may not be those occurring in liquid water because of formation of other radicals from the solute in the case of the electrolyte solution glass and/or perturbation of the water structure by the solute. Furthermore, in slow-cooled aqueous solutions where ice is formed and phase separation of the solute occurs, the radicals trapped in the ice compartments are unable to interact with solutes because these are dissolved in the 'freeze-concentration' regions. These problems can in principle be overcome by investigating water and dilute aqueous solutions in their glassy states which can be obtained by rapid quenching of the liquids. Glassy water can now routinely be made in gram-quantities by so-called 'hyperquenching' of micrometer-sized water droplets on a solid cryoplate. The cooling rates are of the order of 10 6 - 10 7 K s -1 . Our results show that indeed in the hyperquenched dilute aqueous solutions there is no problem with phase separation and radiolysis of hyperquenched water is quite distinct from radiolysis of polycrystalline ice obtained from liquid water quenched in the liquid nitrogen

Fabrication and nano-imprintabilities of Zr-, Pd- and Cu-based glassy alloy thin films

International Nuclear Information System (INIS)

Takenaka, Kana; Saidoh, Noriko; Nishiyama, Nobuyuki; Inoue, Akihisa

2011-01-01

With the aim of investigating nano-imprintability of glassy alloys in a film form, Zr 49 Al 11 Ni 8 Cu 32 , Pd 39 Cu 29 Ni 13 P 19 and Cu 38 Zr 47 Al 9 Ag 6 glassy alloy thin films were fabricated on Si substrate by a magnetron sputtering method. These films exhibit a very smooth surface, a distinct glass transition phenomenon and a large supercooled liquid region of about 80 K, which are suitable for imprinting materials. Moreover, thermal nano-imprintability of these obtained films is demonstrated by using a dot array mold with a dot diameter of 90 nm. Surface observations revealed that periodic nano-hole arrays with a hole diameter of 90 nm were successfully imprinted on the surface of these films. Among them, Pd-based glassy alloy thin film indicated more precise pattern imprintability, namely, flatter residual surface plane and sharper hole edge. It is said that these glassy alloy thin films, especially Pd-based glassy alloy thin film, are one of the promising materials for fabricating micro-machines and nano-devices by thermal imprinting.

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.

Improvement in minimum detectable activity for low energy gamma by optimization in counting geometry

Directory of Open Access Journals (Sweden)

Anil Gupta

2017-01-01

Full Text Available Gamma spectrometry for environmental samples of low specific activities demands low minimum detection levels of measurement. An attempt has been made to lower the gamma detection level of measurement by optimizing the sample geometry, without compromising on the sample size. Gamma energy of 50–200 keV range was chosen for the study, since low energy gamma photons suffer the most self-attenuation within matrix. The simulation study was carried out using MCNP based software “EffCalcMC” for silica matrix and cylindrical geometries. A volume of 250 ml sample geometry of 9 cm diameter is optimized as the best suitable geometry for use, against the in-practice 7 cm diameter geometry of same volume. An increase in efficiency of 10%–23% was observed for the 50–200 keV gamma energy range and a corresponding lower minimum detectable activity of 9%–20% could be achieved for the same.

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.

The energy landscape of glassy dynamics on the amorphous hafnium diboride surface

Science.gov (United States)

Nguyen, Duc; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Girolami, Gregory S.; Lyding, Joseph; Gruebele, Martin

2014-11-01

Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses.

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 .

Structural characterization and aging of glassy pharmaceuticals made using acoustic levitation.

Science.gov (United States)

Benmore, Chris J; Weber, J K R; Tailor, Amit N; Cherry, Brian R; Yarger, Jeffery L; Mou, Qiushi; Weber, Warner; Neuefeind, Joerg; Byrn, Stephen R

2013-04-01

Here, we report the structural characterization of several amorphous drugs made using the method of quenching molten droplets suspended in an acoustic levitator. (13) C NMR, X-ray, and neutron diffraction results are discussed for glassy cinnarizine, carbamazepine, miconazole nitrate, probucol, and clotrimazole. The (13) C NMR results did not find any change in chemical bonding induced by the amorphization process. High-energy X-ray diffraction results were used to characterize the ratio of crystalline to amorphous material present in the glasses over a period of 8 months. All the glasses were stable for at least 6 months except carbamazepine, which has a strong tendency to crystallize within a few months. Neutron and X-ray pair distribution function analyses were applied to the glassy materials, and the results were compared with their crystalline counterparts. The two diffraction techniques yielded similar results in most cases and identified distinct intramolecular and intermolecular correlations. The intramolecular scattering was calculated based on the crystal structure and fit to the measured X-ray structure factor. The resulting intermolecular pair distribution functions revealed broad-nearest and next-nearest neighbor molecule-molecule correlations. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1290-1300, 2013. Copyright © 2013 Wiley Periodicals, Inc.

Immobilization of DNA at Glassy Ccarbon Electrodes: A Critical Study of Adsorbed Layer

Directory of Open Access Journals (Sweden)

G. A. Rivas

2005-11-01

Full Text Available In this work we present a critical study of the nucleic acid layer immobilized atglassy carbon electrodes. Different studies were performed in order to assess the nature of theinteraction between DNA and the electrode surface. The adsorption and electrooxidation of DNAdemonstrated to be highly dependent on the surface and nature of the glassy carbon electrode. TheDNA layer immobilized at a freshly polished glassy carbon electrode was very stable even afterapplying highly negative potentials. The electron transfer of potassium ferricyanide, catechol anddopamine at glassy carbon surfaces modified with thin (obtained by adsorption under controlledpotential conditions and thick (obtained by casting the glassy carbon surface with highly concentratedDNA solutions DNA layers was slower than that at the bare glassy carbon electrode, although thiseffect was dependent on the thickness of the layer and was not charge selective. Raman experimentsshowed an important decrease of the vibrational modes assigned to the nucleobases residues,suggesting a strong interaction of these residues with the electrode surface. The hybridization ofoligo(dG21 and oligo(dC21 was evaluated from the guanine oxidation signal and the reduction of theredox indicator Co(phen33+ . In both cases the chronopotentiometric response indicated that thecompromise of the bases in the interaction of DNA with the electrode surface is too strong, preventingfurther hybridization. In summary, glassy carbon is a useful electrode material to detect DNA in adirect and very sensitive way, but not to be used for the preparation of biorecognition layers by directadsorption of the probe sequence on the electrode surface for detecting the hybridization event.

Levy-free part in energy tax is not wanted

International Nuclear Information System (INIS)

Gilijamse, W.

1995-01-01

The Dutch government proposed to implement an energy levy for small-scale consumers in 1996. The yields will be reimbursed by means of a reduction of the tax burden. By applying a levy-free tax allowance the tax reduction can be limited. However, it appears that this allowance does not work: it reduces the energy saving impact of the energy levy, because it does not stimulate investments in energy saving housing construction and energy saving heat supply. It also interferes with a just compensation of income. It is recommended to cancel the levy-free tax allowance and to realize compensation by raising the tax free allowance in the income tax. 2 figs., 1 tab., 6 refs

Cost-benefit analysis of implementing minimum energy efficiency standards for household refrigerator-freezers in Malaysia

International Nuclear Information System (INIS)

Mahlia, T.M.I.; Masjuki, H.H.; Saidur, R.; Amalina, M.A.

2004-01-01

The ownership of household electrical appliances especially refrigerator-freezer has increased rapidly in Malaysia. Almost every household in this country has a refrigerator-freezer. To reduce energy consumption in this sector the refrigerator is one of the top priorities of the energy efficiency program for household appliances. Malaysian authority is considering implementing minimum energy efficiency standards for refrigerator-freezer sometime in the coming year. This paper attempts to analyze cost-benefit of implementing minimum energy efficiency standards for household refrigerator-freezers in Malaysia. The calculations were made based on growth of ownership data for refrigerators in Malaysian households. The number of refrigerator-freezer has increased from 175,842 units in 1970 to 4,196,486 in 2000 and it will be about 11,293,043 in the year of 2020. Meanwhile it has accounted for about 26.3% of electricity consumption in a single household. Therefore, efficiency improvement of this appliance will give a significant impact in the future of electricity consumption in this country. Furthermore, it has been found that implementing an energy efficiency standard for household refrigerator-freezers is economically justified

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

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

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

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.

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.

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

Spatially heterogeneous ages in glassy dynamics

International Nuclear Information System (INIS)

Castillo, Horacio E.; Chamon, Claudio Chamon; Cugliandolo, Leticia F.; Iguain, Jose Luis; Kennett, Malcolm P.

2003-09-01

We construct a framework for the study of fluctuations in the nonequilibrium relaxation of glassy systems with and without quenched disorder. We study two types of two-time local correlators with the aim of characterizing the heterogeneous evolution in these systems: in one case we average the local correlators over histories of the thermal noise, in the other case we simply coarse-grain the local correlators obtained for a given noise realization. We explain why the noise-averaged correlators describe the fingerprint of quenched disorder when it exists, while the coarse-grained correlators are linked to noise-induced mesoscopic fluctuations. We predict constraints on the distribution of the fluctuations of the coarse-grained quantities. In particular, we show that locally defined correlations and responses are connected by a generalized local out-of-equilibrium fluctuation-dissipation relation. We argue that large size heterogeneities in the age of the system survive in the long-time limit. A symmetry of the underlying theory, namely invariance under reparametrizations of the time coordinates, underlies these results. We establish a connection between the probabilities of spatial distributions of local coarse-grained quantities and the theory of dynamic random manifolds. We define, and discuss the behavior of, a two-time dependent correlation length from the spatial decay of the fluctuations in the two-time local functions. We characterize the fluctuations in the system in terms of their fractal properties. For concreteness, we present numerical tests performed on disordered spin models in finite and infinite dimensions. Finally, we explain how these ideas can be applied to the analysis of the dynamics of other glassy systems that can be either spin models without disorder or atomic and molecular glassy systems. (author)

c-T phase diagram and Landau free energies of (AgAu)55 nanoalloy via neural-network molecular dynamic simulations.

Science.gov (United States)

Chiriki, Siva; Jindal, Shweta; Bulusu, Satya S

2017-10-21

For understanding the structure, dynamics, and thermal stability of (AgAu) 55 nanoalloys, knowledge of the composition-temperature (c-T) phase diagram is essential due to the explicit dependence of properties on composition and temperature. Experimentally, generating the phase diagrams is very challenging, and therefore theoretical insight is necessary. We use an artificial neural network potential for (AgAu) 55 nanoalloys. Predicted global minimum structures for pure gold and gold rich compositions are lower in energy compared to previous reports by density functional theory. The present work based on c-T phase diagram, surface area, surface charge, probability of isomers, and Landau free energies supports the enhancement of catalytic property of Ag-Au nanoalloys by incorporation of Ag up to 24% by composition in Au nanoparticles as found experimentally. The phase diagram shows that there is a coexistence temperature range of 70 K for Ag 28 Au 27 compared to all other compositions. We propose the power spectrum coefficients derived from spherical harmonics as an order parameter to calculate Landau free energies.

Dielectric relaxation in glassy Se75In25− xPbx alloys

Indian Academy of Sciences (India)

In this paper we report the effect of Pb incorporation in the dielectric properties of a-Se75In25 glassy alloy. The temperature and frequency dependence of the dielectric constants and the dielectric losses in glassy Se75In25−Pb ( = 0, 5, 10 and 15) alloys in the frequency range (1 kHz–5 MHz) and temperature range ...

Corrosion fatigue studies on a bulk glassy Zr-based alloy under three-point bending

Science.gov (United States)

Grell, Daniel; Wilkin, Yannic; Gostin, Petre F.; Gebert, Annett; Kerscher, Eberhard

2016-12-01

Corrosion fatigue (CF) tests were carried out on bulk glassy Zr52.5Cu17.9Al10Ni14.6Ti5 (Vitreloy 105) samples under load-controlled three-point bending conditions with a load ratio of R = 0.1 in 0.01 M Na2SO4 + 0.01 M NaCl electrolyte. During cyclic testing, the bar-shaped specimens were polarized in situ at constant potentials and the current was monitored. Three different anodic potentials within the interval between the pitting potential EP and the repassivation potential ER, and three different load amplitudes were applied. In some cases, in situ microscopic observations revealed the formation of black corrosion products in the vicinity of the crack tip during anodic polarization. Fractographic analysis revealed a clear distinction between two modes of crack growth characterized by smooth dissolution induced regions on the one hand and slim fast fracture areas on the other hand. Both alternating features contributed to a broad striated corrosion fatigue fracture surface. Moreover, further fatigue tests were carried out under free corrosion conditions yielding additional information on crack initiation and crack propagation period by means of the open circuit potential (OCP) changes. Thereby, a slight increase in OCP was detected after rupture of the passive layer due to bare metal exposed to the electrolyte. The electrochemical response increased continuously according to stable crack propagation until fracture occurred. Finally, the fracture surfaces of the corrosion fatigue samples were investigated by energy dispersive X-ray with the objective of analyzing the elemental distribution after anodic dissolution. Interestingly, anodic polarization at a near repassivation potential of -50 mV vs. SCE (Saturated Calomel Electrode, E = 0.241 V vs. SHE, Standard Hydrogen Electrode) led to favorable effects on the fatigue lifetime. In conclusion, all results are conflated to a corrosion fatigue model for bulk glassy Vitreloy 105 under anodic polarization in chloride

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.

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.)

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.

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.

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.

Reliability analysis of minimum energy on target for laser facilities with more beam lines

International Nuclear Information System (INIS)

Chen Guangyu

2008-01-01

Shot reliability performance measures of laser facilities with more beam lines pertain to three categories: minimum-energy-on-target, power balance, and shot diagnostics. Accounting for symmetry of NIF beam line design and similarity of subset reliability in a same partition, a fault tree of meeting minimum-energy-on-target for the large laser facility shot of type K and a simplified method are presented, which are used to analyze hypothetic reliability of partition subsets in order to get trends of influences increasing number of beam lines and diverse shot types of large laser facilities on their shot reliability. Finally, it finds that improving component reliability is more crucial for laser facilities with more beam lines in comparison with those with beam lines and functional diversity from design flexibility is greatly helpful for improving shot reliability. (authors)

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.

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.

Attainability and minimum energy of single-stage membrane and membrane/distillation hybrid processes

KAUST Repository

Alshehri, Ali

2014-12-01

As an energy-efficient separation method, membrane technology has attracted more and more attentions in many challenging separation processes. The attainability and the energy consumption of a membrane process are the two basic fundamental questions that need to be answered. This report aims to use process simulations to find: (1) at what conditions a single-stage membrane process can meet the separation task that is defined by product purity and recovery ratio and (2) what are the most important parameters that determine the energy consumption. To perform a certain separation task, it was found that both membrane selectivity and pressure ratio exhibit a minimum value that is defined only by product purity and recovery ratio. The membrane/distillation hybrid system was used to study the energy consumption. A shortcut method was developed to calculate the minimum practical separation energy (MPSE) of the membrane process and the distillation process. It was found that the MPSE of the hybrid system is only determined by the membrane selectivity and the applied transmembrane pressure ratio in three stages. At the first stage when selectivity is low, the membrane process is not competitive to the distillation process. Adding a membrane unit to a distillation tower will not help in reducing energy. At the second medium selectivity stage, the membrane/distillation hybrid system can help reduce the energy consumption, and the higher the membrane selectivity, the lower is the energy. The energy conservation is further improved as pressure ratio increases. At the third stage when both selectivity and pressure ratio are high, the hybrid system will change to a single-stage membrane unit and this change will cause significant reduction in energy consumption. The energy at this stage keeps decreasing with selectivity at slow rate, but slightly increases with pressure ratio. Overall, the higher the membrane selectivity, the more the energy is saved. Therefore, the two

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.

Free neutron-proton analyzing power at medium energies

International Nuclear Information System (INIS)

Newsom, C.R.

1980-01-01

In recent years, increasing efforts have been made to measure the nucleon-nucleon polarization parameters. To date, no free neutron-proton spin correlated parameters have been published in the energy range 500 to 800 MeV. Existing analyzing power data is of low precision and in most cases was obtained by quasi-free proton scattering. As a first step in determining the neutron-proton scattering matrix, the free neutron-proton analyzing power has been measured at the Los Alamos Physics Facility as a function of energy and angle. The experiment was performed by scattering a neutron beam from a polarized proton target. The neutron beam was generated by scattering 800 MeV protons from a Beryllium target and using the neutrons produced at 0 degrees. The incident energy ranged from 300 MeV to 800 MeV. The energy spread of the neutron beam made it possible to measure the analyzing power at different energies simultaneously. Angular distributions were taken from 60 to 170 degrees in the center of mass system (c.m.)

Minimum additive waste stabilization using vitreous ceramics. Progress report, October 1994--September 1995

International Nuclear Information System (INIS)

Feng, X.; Hahn, W.K.; Gong, M.; Gong, W.; Wang, L.; Ewing, R.C.

1995-01-01

Vitreous ceramic waste forms are being developed at Pacific Northwest Laboratory to complement glass waste forms in implementing the Minimum Additive Waste Stabilization (MAWS) Program to support the US Department of Energy's environmental restoration efforts. These vitreous ceramics are composed of various metal-oxide crystalline phases embedded in a silicate-glass phase. This work extends the success of vitreous ceramic waste forms to treat wastes with both high metal and high alkali contents. Two successful approaches are discussed: developing high-durability alkali-binding crystals in a durable glassy matrix, and developing water-soluble crystals in a durable and continuous glassy matrix. Nepheline-vitreous ceramics were demonstrated for the immobilization of high-alkali wastes with alkali contents up to 21 wt%. The chemical durability of the nepheline-vitreous ceramics is better than the corresponding glasses, especially in over longer times. Vitreous ceramics with Cs 2 O loading up to 35.4 wt% have been developed. Vitreous ceramic waste forms were developed from 90 and 100% Oak Ridge National Laboratory K-25 pond sludge. Heat treatment resulted in targeted crystal formation of spinels, potassium feldspar, and Ca-P phases. The K-25 pond sludge vitreous ceramics were up to 42 times more durable than high-level environmental assessments (EA) glass. The toxicity characteristics leach procedure (TCLP) concentration of LVC-6 is at least 2,000 times lower than US Environmental Protection Agency limits. Idaho Chemical Process Plant (ICPP) calcined wastes were immobilized into vitreous ceramics with calcine loading up to 88%. These ICPP-vitreous ceramics were more durable than the EA glass by factors of 5 to 30. Vitreous ceramic waste forms are being developed to complement, not to replace, glass waste forms

Potentiometric application of boron- and phosphorus-doped glassy carbon electrodes

Directory of Open Access Journals (Sweden)

ZORAN V. LAUSEVIC

2001-03-01

Full Text Available Acomparative study was carried out of the potentiometric application of boronand phosphorus-doped and undoped glassy carbon samples prepared at the same heat treatment temperature (HTT 1000°C. The electrochemical activities of the obtained electrode materials were investigated on the example of argentometric titrations. It was found that the electrochemical behaviour of the doped glassy carbon samples are very similar to a Sigri (undoped glassy carbon sample (HTT 2400°C. The experiments showed that the potentiometric response depends on the polarization mode, the nature of the sample, the pretreatment of the electrode surface, and the nature of the supporting electrolyte. The amounts of iodide, bromide, and of chloridewere determined to be 1.27 mg, 0.80 mg and 0.54 mg, respectively, with a maximum relative standard deviation of less than 1.1%. The obtained results are in good agreement with the results of comparative potentiometric titrations using a silver indicator electrode. The titrationmethod was applied to the indirect determination of pyridoxine hydrochloride, i.e., vitamin B6.

mwnts composite film modified glassy carbon electrode

African Journals Online (AJOL)

Preferred Customer

ABSTRACT: A poly p-aminosalicylic acid (Poly(p-ASA)) and multiwall carbon nanotubes. (MWCNTs) composite modified glassy carbon (GC) electrode was constructed by casting the MWNTs on the GC electrode surface followed by electropolymerization of the p-ASA on the MWCNTs/GCE. The electrochemical behaviours ...

Voltammetric pH sensing using carbon electrodes: glassy carbon behaves similarly to EPPG.

Science.gov (United States)

Lu, Min; Compton, Richard G

2014-09-21

Developing and building on recent work based on a simple sensor for pH determination using unmodified edge plane pyrolytic graphite (EPPG) electrodes, we present a voltammetric method for pH determination using a bare unmodified glassy carbon (GC) electrode. By exploiting the pH sensitive nature of quinones present on carbon edge-plane like sites within the GC, we show how GC electrodes can be used to measure pH. The electro-reduction of surface quinone groups on the glassy carbon electrode was characterised using cyclic voltammetry (CV) and optimised with square-wave voltammetry (SWV) at 298 K and 310 K. At both temperatures, a linear correlation was observed, corresponding to a 2 electron, 2 proton Nernstian response over the aqueous pH range 1.0 to 13.1. As such, unmodified glassy carbon electrodes are seen to be pH dependent, and the Nernstian response suggests its facile use for pH sensing. Given the widespread use of glassy carbon electrodes in electroanalysis, the approach offers a method for the near-simultaneous measurement and monitoring of pH during such analyses.

Excess free volume in metallic glasses measured by X-ray diffraction

International Nuclear Information System (INIS)

Yavari, Alain Reza; Moulec, Alain Le; Inoue, Akihisa; Nishiyama, Nobuyuki; Lupu, Nicoleta; Matsubara, Eiichiro; Botta, Walter Jose; Vaughan, Gavin; Di Michiel, Marco; Kvick, Ake

2005-01-01

In crystalline materials, lattice expansion as measured by diffraction methods differs from the expansion of the sample dimensions as measured by dilatometry, due to the contribution of thermal vacancies to the latter. We have found that in glassy materials and metallic glasses in particular, this is not the case for the contribution of free volume. These findings are the first direct experimental confirmation of simulation results indicating that atomic size holes are unstable in glasses such that free volume is dispersed randomly. This allows direct measurement of excess free volume in glasses using diffraction methods in place of dilatometry, which is difficult to use once the sample softens at the glass transition temperature T g and above. Quenched-in and deformation-induced free-volume ΔV f were measured by X-ray diffraction in transmission during heating using synchrotron light. The measured thermal expansion coefficients α th were the same as in dilatometry. The glass transition T g appeared as a break in the value of α th at T g . The 'change-of-slope method' was applied to the kinetics of relaxation to derive the activation energy for the free-volume annihilation process

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

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.

Anomalous Capacitance Maximum of the Glassy Carbon-Ionic Liquid Interface through Dilution with Organic Solvents.

Science.gov (United States)

Bozym, David J; Uralcan, Betül; Limmer, David T; Pope, Michael A; Szamreta, Nicholas J; Debenedetti, Pablo G; Aksay, Ilhan A

2015-07-02

We use electrochemical impedance spectroscopy to measure the effect of diluting a hydrophobic room temperature ionic liquid with miscible organic solvents on the differential capacitance of the glassy carbon-electrolyte interface. We show that the minimum differential capacitance increases with dilution and reaches a maximum value at ionic liquid contents near 5-10 mol% (i.e., ∼1 M). We provide evidence that mixtures with 1,2-dichloroethane, a low-dielectric constant solvent, yield the largest gains in capacitance near the open circuit potential when compared against two traditional solvents, acetonitrile and propylene carbonate. To provide a fundamental basis for these observations, we use a coarse-grained model to relate structural variations at the double layer to the occurrence of the maximum. Our results reveal the potential for the enhancement of double-layer capacitance through dilution.

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.

Galactic Cosmic-Ray Energy Spectra and Composition during the 2009-2010 Solar Minimum Period

Science.gov (United States)

Lave, K. A.; Wiedenbeck, Mark E.; Binns, W. R.; Christian, E. R.; Cummings, A. C.; Davis, A. J.; deNolfo, G. A.; Israel, M. H..; Leske, R. A.; Mewaldt, R. A.;

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

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.

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.

Thermodynamic Modeling of Gas Transport in Glassy Polymeric Membranes.

Science.gov (United States)

Minelli, Matteo; Sarti, Giulio Cesare

2017-08-19

Solubility and permeability of gases in glassy polymers have been considered with the aim of illustrating the applicability of thermodynamically-based models for their description and prediction. The solubility isotherms are described by using the nonequilibrium lattice fluid (NELF) (model, already known to be appropriate for nonequilibrium glassy polymers, while the permeability isotherms are described through a general transport model in which diffusivity is the product of a purely kinetic factor, the mobility coefficient, and a thermodynamic factor. The latter is calculated from the NELF model and mobility is considered concentration-dependent through an exponential relationship containing two parameters only. The models are tested explicitly considering solubility and permeability data of various penetrants in three glassy polymers, PSf, PPh and 6FDA-6FpDA, selected as the reference for different behaviors. It is shown that the models are able to calculate the different behaviors observed, and in particular the permeability dependence on upstream pressure, both when it is decreasing as well as when it is increasing, with no need to invoke the onset of additional plasticization phenomena. The correlations found between polymer and penetrant properties with the two parameters of the mobility coefficient also lead to the predictive ability of the transport model.

Minimum Energy Dwelling (MED) workbook: an investigation of techniques and materials for energy conscious design

Energy Technology Data Exchange (ETDEWEB)

1977-12-01

This workbook is based upon information gathered during the design phase of the Minimum Energy Dwelling. The objective of the project, sponsored by the Southern California Gas Co., Department of Energy, and Mission Viejo is to substantially reduce energy use by the incorporation of energy conservation and solar techniques in a single-family detached dwelling. The Project will demonstrate to builders, as well as to the general public, a number of technological innovations that can, at reasonable cost, be included in a dwelling design. The problem facing Southern California Gas Co., along with most other gas utilities, is ever-decreasing amounts of gas at increasing prices. The dwelling designed has approximately 1,150 ft/sup 2/, consistent with current home-building trends. Through the optimum use of energy-conserving appliances, insulation, window and wall shading, exterior coloring, and thermal mass, the yearly energy usage has been reduced by over 50%. Of the remaining 50% of the energy required for heating, cooling, and domestic hot water, the majority is supplied by the solar-energy system. Three hundred twenty square feet (270 effective) of evacuated tube collector are incorporated into the building structure. The hot water provided by the collectors is used to run an absorption chiller for cooling, the domestic hot water, and the heating system. The remaining energy requirements are met by an auxiliary natural gas energy system and a cool-air-economizer cycle.

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.

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

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.

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).

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).

Control of minimum member size in parameter-free structural shape optimization by a medial axis approximation

Science.gov (United States)

Schmitt, Oliver; Steinmann, Paul

2017-09-01

We introduce a manufacturing constraint for controlling the minimum member size in structural shape optimization problems, which is for example of interest for components fabricated in a molding process. In a parameter-free approach, whereby the coordinates of the FE boundary nodes are used as design variables, the challenging task is to find a generally valid definition for the thickness of non-parametric geometries in terms of their boundary nodes. Therefore we use the medial axis, which is the union of all points with at least two closest points on the boundary of the domain. Since the effort for the exact computation of the medial axis of geometries given by their FE discretization highly increases with the number of surface elements we use the distance function instead to approximate the medial axis by a cloud of points. The approximation is demonstrated on three 2D examples. Moreover, the formulation of a minimum thickness constraint is applied to a sensitivity-based shape optimization problem of one 2D and one 3D model.

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

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

The Planck-Benzinger thermal work function in the condensation of water vapor

Science.gov (United States)

Chun, Paul W.

Based on the Planck-Benzinger thermal work function using Chun's method, the innate temperature-invariant enthalpy at 0 K, ?H0(T0), for the condensation of water vapor as well as the dimer, trimer, tetramer, and pentamer form in the vapor phase, was determined to be 0.447 kcal mol-1 for vapor, 1.127 for the dimer, 0.555 for the trimer, 0.236 for the tetramer, and 0.079 kcal mol-1 for the pentamer using ?G(T) data reported by Kell et al. in 1968 and Kell and McLaurin in 1969. These results suggest that the predominant dimeric form is the most stable of these n-mers. Using Nemethy and Scheraga's 1962 data for the Helmholtz free energy of liquid water, the value of ?H0(T0) was determined to be 1.21 kcal mol-1. This is very close to the value for the energy of the hydrogen bond EH of 1.32 kcal mol-1 reported by Nemethy and Scheraga, using statistical thermodynamics. It seems clear that very little energy is required for interconversion between the hypothetical supercooled water vapor and glassy water at 0 K. A hypothetical supercooled water vapor at 0 K is apparently almost as highly associated as glassy water at that temperature, suggesting a dynamic equilibrium between vapor and liquid. This water vapor condensation is highly similar in its thermodynamic behavior to that of sequence-specific pairwise (dipeptide) hydrophobic interaction, except that the negative Gibbs free energy change minimum at ?Ts?, the thermal setpoint for vapor condensation, where T?S = 0, occurs at a considerably lower temperature, 270 K (below 0°C) compared with ?350 K. The temperature of condensation ?Tcond? at which ?G(T) = 0, where water vapor begins to condense, was found to be 383 K. In the case of a sequence-specific pairwise hydrophobic interaction, the melting temperature, ?Tm?, where ?G(Tm) = 0 was found to be 460 K. Only between two temperature limits, ?Th? = 99 K and ?Tcond? = 383 K, where ?G(Tcond) = 0, is the net chemical driving force favorable for polymorphism of glassy water

Relation between time-temperature transformation and continuous heating transformation diagrams of metallic glassy alloys

International Nuclear Information System (INIS)

Louzguine-Luzgin, Dmitri V.; Inoue, Akihisa

2005-01-01

The time-temperature transformation (TTT) diagrams for the onset of devitrification of the Ge-Ni-La and Cu-Hf-Ti glassy alloys were calculated from the isothermal differential calorimetry data using an Arrhenius equation. The continuous heating transformation (CHT) diagrams for the onset of devitrification of the glassy alloys were subsequently recalculated from TTT diagrams. The recalculation method used for conversion of the TTT into CHT diagrams produces reasonable results and is not sensitive to the type of the devitrification reaction (polymorphous or primary transformation). The diagrams allow to perform a comparison of the stabilities of glassy alloys on a long-term scale. The relationship between these diagrams is discussed

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)...

Playback interference of glassy-winged sharp shooter communication

Science.gov (United States)

Animal communication is vital to reproduction, particularly for securing a mate. Insects commonly communicate by exchanging vibrational signals that are transmitted through host plants. The glassy-winged sharpshooter (GWSS), Homalodisca vitripennis, is an important vector of Xylella fastidiosa, a pl...

Glassy selenium at high pressure: Le Chatelier's principle still works

Science.gov (United States)

Brazhkin, V. V.; Tsiok, O. B.

2017-10-01

Selenium is the only easily vitrified elementary substance. Numerous experimental studies of glassy Se (g -Se) at high pressures show a large spread in the data on the compressibility and electrical resistivity of g -Se. Furthermore, H. Liu et al. [Proc. Natl. Acad. Sci. USA 105, 13229 (2008), 10.1073/pnas.0806857105] have arrived at the surprising conclusion that the volume of glass increases during pressure-induced crystallization. We have performed high-precision measurements of the specific volume and electrical resistivity of glassy selenium (g -Se) at high hydrostatic pressures up to 9 GPa. The measured bulk modulus at normal pressure is B =(9.0 5 ±0.15 ) GPa and its pressure derivative is BP'=6.4 ±0.2 . In the pressure range P <3 GPa, glassy selenium has an anomalously large negative second derivative of the bulk modulus. The electrical resistivity of g -Se decreases almost exponentially with increasing pressure and reaches 20 Ω cm at a pressure of 8.75 GPa. The inelastic behavior and weak relaxation of the volume for g -Se begin at pressures above 3.5 GPa; the volume and logarithm of the electrical resistivity relax significantly (logarithmically with the time) at pressures above 8 GPa. Bulk measurements certainly indicate that the volume of g -Se glass in the crystallization pressure range is larger than the volumes of both appearing crystalline phases (by 2% and 4%). Therefore, the "volume expansion phenomenon" suggested in [H. Liu et al., Proc. Natl. Acad. Sci. USA 105, 13229 (2008), 10.1073/pnas.0806857105] is not observed, and the pressure-induced crystallization of glassy selenium is consistent with the laws of thermodynamics.

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…

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.

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.

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.

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.

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory

Science.gov (United States)

Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth; Star, Keith; Baker, Nathan A.

2016-01-01

There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of “maximum flow-minimum cut” graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein, and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial-time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered. PMID:27089174

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory.

Science.gov (United States)

Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth; Star, Keith; Baker, Nathan A

2016-08-25

There are several applications in computational biophysics that require the optimization of discrete interacting states, for example, amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of "maximum flow-minimum cut" graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered.

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

How Glassy States Affect Brown Carbon Production?

Science.gov (United States)

Liu, P.; Li, Y.; Wang, Y.; Bateman, A. P.; Zhang, Y.; Gong, Z.; Gilles, M. K.; Martin, S. T.

2015-12-01

Secondary organic material (SOM) can become light-absorbing (i.e. brown carbon) via multiphase reactions with nitrogen-containing species such as ammonia and amines. The physical states of SOM, however, potentially slow the diffusion of reactant molecules in organic matrix under conditions that semisolids or solids prevail, thus inhibiting the browning reaction pathways. In this study, the physical states and the in-particle diffusivity were investigated by measuring the evaporation kinetics of both water and organics from aromatic-derived SOMs using a quartz-crystal-microbalance (QCM). The results indicate that the SOMs derived from aromatic precursors toluene and m-xylene became solid (glassy) and the in particle diffusion was significantly impeded for sufficiently low relative humidity ( toluene-derived SOM after ammonia exposure at varied RHs. The results suggest that the production of light-absorbing nitrogen-containing compounds from multiphase reactions with ammonia was kinetically limited in the glassy organic matrix, which otherwise produce brown carbon. The results of this study have significant implications for production and optical properties of brown carbon in urban atmospheres that ultimately influence the climate and tropospheric photochemistry.

Shear-transformation-zone theory of linear glassy dynamics.

Science.gov (United States)

Bouchbinder, Eran; Langer, J S

2011-06-01

We present a linearized shear-transformation-zone (STZ) theory of glassy dynamics in which the internal STZ transition rates are characterized by a broad distribution of activation barriers. For slowly aging or fully aged systems, the main features of the barrier-height distribution are determined by the effective temperature and other near-equilibrium properties of the configurational degrees of freedom. Our theory accounts for the wide range of relaxation rates observed in both metallic glasses and soft glassy materials such as colloidal suspensions. We find that the frequency-dependent loss modulus is not just a superposition of Maxwell modes. Rather, it exhibits an α peak that rises near the viscous relaxation rate and, for nearly jammed, glassy systems, extends to much higher frequencies in accord with experimental observations. We also use this theory to compute strain recovery following a period of large, persistent deformation and then abrupt unloading. We find that strain recovery is determined in part by the initial barrier-height distribution, but that true structural aging also occurs during this process and determines the system's response to subsequent perturbations. In particular, we find by comparison with experimental data that the initial deformation produces a highly disordered state with a large population of low activation barriers, and that this state relaxes quickly toward one in which the distribution is dominated by the high barriers predicted by the near-equilibrium analysis. The nonequilibrium dynamics of the barrier-height distribution is the most important of the issues raised and left unresolved in this paper.

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.

Optimization of Operating Parameters for Minimum Mechanical Specific Energy in Drilling

Energy Technology Data Exchange (ETDEWEB)

Hamrick, Todd [West Virginia Univ., Morgantown, WV (United States)

2011-01-01

Efficiency in drilling is measured by Mechanical Specific Energy (MSE). MSE is the measure of the amount of energy input required to remove a unit volume of rock, expressed in units of energy input divided by volume removed. It can be expressed mathematically in terms of controllable parameters; Weight on Bit, Torque, Rate of Penetration, and RPM. It is well documented that minimizing MSE by optimizing controllable factors results in maximum Rate of Penetration. Current methods for computing MSE make it possible to minimize MSE in the field only through a trial-and-error process. This work makes it possible to compute the optimum drilling parameters that result in minimum MSE. The parameters that have been traditionally used to compute MSE are interdependent. Mathematical relationships between the parameters were established, and the conventional MSE equation was rewritten in terms of a single parameter, Weight on Bit, establishing a form that can be minimized mathematically. Once the optimum Weight on Bit was determined, the interdependent relationship that Weight on Bit has with Torque and Penetration per Revolution was used to determine optimum values for those parameters for a given drilling situation. The improved method was validated through laboratory experimentation and analysis of published data. Two rock types were subjected to four treatments each, and drilled in a controlled laboratory environment. The method was applied in each case, and the optimum parameters for minimum MSE were computed. The method demonstrated an accurate means to determine optimum drilling parameters of Weight on Bit, Torque, and Penetration per Revolution. A unique application of micro-cracking is also presented, which demonstrates that rock failure ahead of the bit is related to axial force more than to rotation speed.

Electrochemical oxidation of niclosamide at a glassy carbon ...

African Journals Online (AJOL)

Cyclic voltammetry, square-wave voltammetry and controlled potential electrolysis have been used to study the electrochemical oxidation behaviour of niclosamide at a glassy carbon electrode. The number of electrons transferred, the wave characteristics, the diffusion coefficient and reversibility of the reactions have been ...

Au55, a stable glassy cluster: results of ab initio calculations

Directory of Open Access Journals (Sweden)

Dieter Vollath

2017-10-01

Full Text Available Structure and properties of small nanoparticles are still under discussion. Moreover, some thermodynamic properties and the structural behavior still remain partially unknown. One of the best investigated nanoparticles is the Au55 cluster, which has been analyzed experimentally and theoretically. However, up to now, the results of these studies are still inconsistent. Consequently, we have carried out the present ab initio study of the Au55 cluster, using up-to-date computational concepts, in order to clarify these issues. Our calculations have confirmed the experimental result that the thermodynamically most stable structure is not crystalline, but it is glassy. The non-crystalline structure of this cluster was validated by comparison of the coordination numbers with those of a crystalline cluster. It was found that, in contrast to bulk materials, glass formation is connected to an energy release that is close to the melting enthalpy of bulk gold. Additionally, the surface energy of this cluster was calculated using two different theoretical approaches resulting in values close to the surface energy for bulk gold. It shall be emphasized that it is now possible to give a confidence interval for the value of the surface energy.

Energy Efficiency: The Implementation of Minimum Energy Performance Standard (MEPS Application on Home Appliances for Residential

Directory of Open Access Journals (Sweden)

Rahman K.A

2016-01-01

Full Text Available Generally, Minimum Energy Performance Standard (MEPS has been widespread across the country especially developed country. However, most consumers do not even know about the MEPS. Without sufficient knowledge, much energy have been wasted before this. The aim of this study is to review the implementation of MEPS of Asia country and to compare electricity consumption of home appliances with star rating and without star rating. In order to fulfil the objectives of the study, the equipment must be chosen correctly and must be learned properly. The home appliances that will be used also need to be chosen so that the comparison between the appliances will be matched correctly. To understand the results, the analysis was done using graphs and table. The purpose of using graph and table is to understand the comparison between appliances more clearly. The results show that home appliances with MEPS is more efficient on energy saving rather than without MEPS. This is the evidence as a method to educate a consumer on energy saving.

Glassy carbon supercapacitor: 100,000 cycles demonstrated

Energy Technology Data Exchange (ETDEWEB)

Baertsch, M; Braun, A; Schnyder, B; Koetz, R [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1999-08-01

A 5 V glassy carbon capacitor stack was built consisting of four bipolar and two end-plate electrodes. More than 100,000 charging/discharging cycles were applied to test the stability of the double-layer capacitor. Low and high frequency resistances were measured as a function of the number of cycles. (author) 2 figs., 1 ref.

Model-based and model-free “plug-and-play” building energy efficient control

International Nuclear Information System (INIS)

Baldi, Simone; Michailidis, Iakovos; Ravanis, Christos; Kosmatopoulos, Elias B.

2015-01-01

Highlights: • “Plug-and-play” Building Optimization and Control (BOC) driven by building data. • Ability to handle the large-scale and complex nature of the BOC problem. • Adaptation to learn the optimal BOC policy when no building model is available. • Comparisons with rule-based and advanced BOC strategies. • Simulation and real-life experiments in a ten-office building. - Abstract: Considerable research efforts in Building Optimization and Control (BOC) have been directed toward the development of “plug-and-play” BOC systems that can achieve energy efficiency without compromising thermal comfort and without the need of qualified personnel engaged in a tedious and time-consuming manual fine-tuning phase. In this paper, we report on how a recently introduced Parametrized Cognitive Adaptive Optimization – abbreviated as PCAO – can be used toward the design of both model-based and model-free “plug-and-play” BOC systems, with minimum human effort required to accomplish the design. In the model-based case, PCAO assesses the performance of its control strategy via a simulation model of the building dynamics; in the model-free case, PCAO optimizes its control strategy without relying on any model of the building dynamics. Extensive simulation and real-life experiments performed on a 10-office building demonstrate the effectiveness of the PCAO–BOC system in providing significant energy efficiency and improved thermal comfort. The mechanisms embedded within PCAO render it capable of automatically and quickly learning an efficient BOC strategy either in the presence of complex nonlinear simulation models of the building dynamics (model-based) or when no model for the building dynamics is available (model-free). Comparative studies with alternative state-of-the-art BOC systems show the effectiveness of the PCAO–BOC solution

Observation of glassy state relaxation during annealing of frozen sugar solutions by X-ray computed tomography.

Science.gov (United States)

Nakagawa, Kyuya; Tamiya, Shinri; Do, Gabsoo; Kono, Shinji; Ochiai, Takaaki

2018-06-01

Glassy phase formation in a frozen product determines various properties of the freeze-dried products. When an aqueous solution is subjected to freezing, a glassy phase forms as a consequence of freeze-concentration. During post-freezing annealing, the relaxation of the glassy phase and the ripening of ice crystals (i.e. Ostwald ripening) spontaneously occur, where the kinetics are controlled by the annealing and glass transition temperatures. This study was motivated to observe the progress of glassy state relaxation separate from ice coarsening during annealing. X-ray computed tomography (CT) was used to observe a frozen and post-freezing annealed solutions by using monochromatized X-ray from the synchrotron radiation. CT images were successfully obtained, and the frozen matrix were analyzed based on the gray level values that were equivalent to the linear X-ray attenuation coefficients of the observed matters. The CT images obtained from rapidly frozen sucrose and dextrin solutions with different concentrations gave clear linear relationships between the linear X-ray attenuation coefficients values and the solute concentrations. It was confirmed that the glassy state relaxation progressed as increasing annealing time, and this trend was larger in the order of the glass transition temperature of the maximally freeze-concentrated phase. The sucrose-water system required nearly 20 h of annealing time at -5 °C for the completion of the glassy phase relaxation, whereas dextrin-water systems required much longer periods because of their higher glass transition temperatures. The trends of ice coarsening, however, did not perfectly correspond to the trends of the relaxation, suggesting that the glassy phase relaxation and Ostwald ripening would jointly control the ice crystal growth/ripening kinetics, and the dominant mechanism differed by the annealing stage. Copyright © 2018 Elsevier B.V. All rights reserved.

SUPERNOVA SHOCK-WAVE-INDUCED CO-FORMATION OF GLASSY CARBON AND NANODIAMOND

Energy Technology Data Exchange (ETDEWEB)

Stroud, Rhonda [Naval Research Laboratory, Washington, D.C.; Chisholm, Matthew F [ORNL; Heck, Phillipp [The Field Museum, Chicago, IL; Alexander, Conel [Carnegie Institution of Washington; Nittler, Larry [Carnegie Institution of Washington

2011-01-01

Nanodiamond (ND) was the first extrasolar dust phase to be identified in meteorites. However, the 2 nm average size of the NDs precludes isotopic analysis of individual particles, and thus their origin(s) remains controversial. Using electron microscopy with subnanometer resolution, we show that ND separates from the Allende and Murchison meteorites are actually a two-phase mixture of ND and glassy carbon. This phase mixture is likely the product of supernova shock-wave transformation of pre-formed organics in the interstellar medium (ISM). The glassy carbon ND mixture is also a plausible contributor to the 2175 extinction feature in the diffuse ISM.

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.

An Experimental Setup to Measure the Minimum Trigger Energy for Magneto-Thermal Instability in Nb$_{3}$Sn Strands

CERN Document Server

Takala, E; Bremer, J; Balle, C; Bottura, L; Rossi, L

2012-01-01

Magneto-thermal instability may affect high critical current density Nb$_{3}$Sn superconducting strands that can quench even though the transport current is low compared to the critical current with important implications in the design of next generation superconducting magnets. The instability is initiated by a small perturbation energy which is considerably lower than the Minimum Quench Energy (MQE). At CERN, a new experimental setup was developed to measure the smallest perturbation energy (Minimum Trigger Energy, MTE) which is able to trigger the magneto-thermal instability in superconducting Nb$_{3}$Sn-strands. The setup is based on Q-switched laser technology which is able to provide a localized perturbation in nano-second time scale. Using this technique the energy deposition into the strand is well defined and reliable. The laser is located outside the cryostat at room temperature. The beam is guided from room temperature on to the superconducting strand by using a UV-enhanced fused silica fibre. The ...

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.

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.

Solvated electron structure in glassy matrices

International Nuclear Information System (INIS)

Kevan, L.

1981-01-01

Current knowledge of the detailed geometrical structure of solvated electrons in aqueous and organic media is summarized. The geometry of solvated electrons in glassy methanol, ethanol, and 2-methyltetrahydrofuran is discussed. Advanced electron magnetic resonance methods and development of new methods of analysis of electron spin echo modulation patterns, second moment line shapes, and forbidden photon spin-flip transitions for paramagnetic species in these disordered systems are discussed. 66 references are cited

Diffusion Monte Carlo study on temporal evolution of entropy and free energy in nonequilibrium processes.

Science.gov (United States)

Tanaka, Shigenori

2016-03-07

, we observe a nonequilibrium behavior that the system entropy first increases with the broadening of the initially localized walker distribution and then it begins to decrease along with the trapping at the global minimum of the potential, thus leading to the minimization of the free energy.

Gold nanoparticle/multi-walled carbon nanotube modified glassy carbon electrode as a sensitive voltammetric sensor for the determination of diclofenac sodium

International Nuclear Information System (INIS)

Afkhami, Abbas; Bahiraei, Atousa; Madrakian, Tayyebeh

2016-01-01

A simple and highly sensitive sensor for the determination of diclofenac sodium based on gold nanoparticle/multi-walled carbon nanotube modified glassy carbon electrode is reported. Scanning electron microscopy along with energy dispersive X-ray spectroscopy, electrochemical impedance spectroscopy, cyclic voltammetry and square wave voltammetry was used to characterize the nanostructure and performance of the sensor and the results were compared with those obtained at the multi-walled carbon nanotube modified glassy carbon electrode and bare glassy carbon electrode. Under the optimized experimental conditions diclofenac sodium gave linear response over the range of 0.03–200 μmol L −1 . The lower detection limits were found to be 0.02 μmol L −1 . The effect of common interferences on the current response of DS was investigated. The practical application of the modified electrode was demonstrated by measuring the concentration of diclofenac sodium in urine and pharmaceutical samples. This revealed that the gold nanoparticle/multiwalled carbon nanotube modified glassy carbon electrode shows excellent analytical performance for the determination of diclofenac sodium in terms of a very low detection limit, high sensitivity, very good accuracy, repeatability and reproducibility. - Highlights: • GCE was modified with multiwalled carbon nanotube and gold nanoparticles. • AuNP/MWCNT/GCE was used for the determination of diclofenac sodium. • Modified electrode was characterized by SEM, EDS and EIS. • The proposed method showed excellent analytical figures of merit. • This sensor was used for the determination of diclofenac sodium in real samples.

Gold nanoparticle/multi-walled carbon nanotube modified glassy carbon electrode as a sensitive voltammetric sensor for the determination of diclofenac sodium

Energy Technology Data Exchange (ETDEWEB)

Afkhami, Abbas, E-mail: afkhami@basu.ac.ir; Bahiraei, Atousa; Madrakian, Tayyebeh

2016-02-01

A simple and highly sensitive sensor for the determination of diclofenac sodium based on gold nanoparticle/multi-walled carbon nanotube modified glassy carbon electrode is reported. Scanning electron microscopy along with energy dispersive X-ray spectroscopy, electrochemical impedance spectroscopy, cyclic voltammetry and square wave voltammetry was used to characterize the nanostructure and performance of the sensor and the results were compared with those obtained at the multi-walled carbon nanotube modified glassy carbon electrode and bare glassy carbon electrode. Under the optimized experimental conditions diclofenac sodium gave linear response over the range of 0.03–200 μmol L{sup −1}. The lower detection limits were found to be 0.02 μmol L{sup −1}. The effect of common interferences on the current response of DS was investigated. The practical application of the modified electrode was demonstrated by measuring the concentration of diclofenac sodium in urine and pharmaceutical samples. This revealed that the gold nanoparticle/multiwalled carbon nanotube modified glassy carbon electrode shows excellent analytical performance for the determination of diclofenac sodium in terms of a very low detection limit, high sensitivity, very good accuracy, repeatability and reproducibility. - Highlights: • GCE was modified with multiwalled carbon nanotube and gold nanoparticles. • AuNP/MWCNT/GCE was used for the determination of diclofenac sodium. • Modified electrode was characterized by SEM, EDS and EIS. • The proposed method showed excellent analytical figures of merit. • This sensor was used for the determination of diclofenac sodium in real samples.

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.

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.)

An Improved Optimization Function for Maximizing User Comfort with Minimum Energy Consumption in Smart Homes

Directory of Open Access Journals (Sweden)

Israr Ullah

2017-11-01

Full Text Available In the smart home environment, efficient energy management is a challenging task. Solutions are needed to achieve a high occupant comfort level with minimum energy consumption. User comfort is measured in terms of three fundamental parameters: (a thermal comfort, (b visual comfort and (c air quality. Temperature, illumination and CO 2 sensors are used to collect indoor contextual information. In this paper, we have proposed an improved optimization function to achieve maximum user comfort in the building environment with minimum energy consumption. A comprehensive formulation is done for energy optimization with detailed analysis. The Kalman filter algorithm is used to remove noise in sensor readings by predicting actual parameter values. For optimization, we have used genetic algorithm (GA and particle swarm optimization (PSO algorithms and performed comparative analysis with a baseline scheme on real data collected for a one-month duration in our lab’s indoor environment. Experimental results show that the proposed optimization function has achieved a 27 . 32 % and a 31 . 42 % reduction in energy consumption with PSO and GA, respectively. The user comfort index was also improved by 10 % i.e., from 0 . 86 to 0 . 96 . GA-based optimization results were better than PSO, as it has achieved almost the same user comfort with 4 . 19 % reduced energy consumption. Results show that the proposed optimization function gives better results than the baseline scheme in terms of user comfort and the amount of consumed energy. The proposed system can help with collecting the data about user preferences and energy consumption for long-term analysis and better decision making in the future for efficient resource utilization and overall profit maximization.

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

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

OpenAIRE

Canfield, D. E.; Thamdrup, B.; De Brabandere, L.; Dalsgaard, T.; Revsbech, N. P.; Ulloa, O.; Stewart, Frank J.; DeLong, Edward Francis

2010-01-01

Nitrogen cycling is normally thought to dominate the biogeochemistry and microbial ecology of oxygen-minimum zones in marine environments. Through a combination of molecular techniques and process rate measurements, we showed that both sulfate reduction and sulfide oxidation contribute to energy flux and elemental cycling in oxygen-free waters off the coast of northern Chile. These processes may have been overlooked because in nature, the sulfide produced by sulfate reduction immediately oxid...

Physical properties of Zr50Cu40-xAl10Pdx bulk glassy alloys

International Nuclear Information System (INIS)

Wencka, M.; Jagodic, M.; Gradisek, A.; Kocjan, A.; Jaglicic, Z.; McGuiness, P.J.; Apih, T.; Yokoyama, Y.; Dolinsek, J.

2010-01-01

It was shown recently (Yokoyama et al. ) that the addition of a small amount of Pd to the Zr 50 Cu 40 Al 10 bulk glassy alloy (BGA) has a beneficial effect on fatigue-strength enhancement, where the composition Zr 50 Cu 37 Al 10 Pd 3 behaved in a resonant-like way by showing the highest fatigue limit of 1050 MPa and the minimum Vickers hardness. We performed a study of the magnetic properties, the specific heat, the electrical resistivity and the hydrogen-diffusion constant for a series of compositions Zr 50 Cu 40-x Al 10 Pd x (x = 0-7 at.%), in order to determine their physical properties and to check for the influence of the Pd content on these properties. The Zr 50 Cu 40-x Al 10 Pd x BGAs are nonmagnetic, conducting alloys, where the Pauli spin susceptibility of the conduction electrons is the only source of paramagnetism. The low-temperature specific heat indicates an enhancement of the conduction-electron effective mass m* below 5 K, suggesting that the Zr 50 Cu 40-x Al 10 Pd x BGAs are not free-electron-like compounds. The electrical resistivities of the Zr 50 Cu 40-x Al 10 Pd x BGAs amount to about 200 μΩ cm and show a small, negative temperature coefficient (NTC) with an increase from 300 to 2 K of 4%. The hydrogen self-diffusion constant D in hydrogen-loaded samples shows classical over-barrier-hopping temperature dependence and is of comparable magnitude to the related icosahedral and amorphous Zr 69.5 Cu 12 Ni 11 Al 7.5 hydrogen-storage alloys. No correlation between the investigated physical parameters and the Pd content of the samples could be observed.

Minimum Quench Energy and Early Quench Development in NbTi Superconducting Strands

CERN Document Server

Breschi, M; Boselli, M; Bottura, Luca; Devred, Arnaud; Ribani, P L; Trillaud, F

2007-01-01

The stability of superconducting wires is a crucial task in the design of safe and reliable superconducting magnets. These magnets are prone to premature quenches due to local releases of energy. In order to simulate these energy disturbances, various heater technologies have been developed, such as coated tips, graphite pastes, and inductive coils. The experiments studied in the present work have been performed using a single-mode diode laser with an optical fiber to illuminate the superconducting strand surface. Minimum quench energies and voltage traces at different magnetic flux densities and transport currents have been measured on an LHC-type, Cu/NbTi wire bathed in pool boiling helium I. This paper deals with the numerical analysis of the experimental data. In particular, a coupled electromagnetic and thermal model has been developed to study quench development and propagation, focusing on the influence of heat exchange with liquid helium.

Overview of direct air free cooling and thermal energy storage potential energy savings in data centres

International Nuclear Information System (INIS)

Oró, Eduard; Depoorter, Victor; Pflugradt, Noah; Salom, Jaume

2015-01-01

In the last years the total energy demand of data centres has experienced a dramatic increase which is expected to continue. This is why data centres industry and researchers are working on implementing energy efficiency measures and integrating renewable energy to overcome energy dependence and to reduce operational costs and CO 2 emissions. The cooling system of these unique infrastructures can account for 40% of the total energy consumption. To reduce the energy consumption, free cooling strategies are used more and more, but so far there has been little research about the potential of thermal energy storage (TES) solutions to match energy demand and energy availability. Hence, this work intends to provide an overview of the potential of the integration of direct air free cooling strategy and TES systems into data centres located at different European locations. For each location, the benefit of using direct air free cooling is evaluated energetically and economically for a data centre of 1250 kW. The use of direct air free cooling is shown to be feasible. This does not apply the TES systems by itself. But when using TES in combination with an off-peak electricity tariff the operational cooling cost can be drastically reduced. - Highlights: • The total annual hours for direct air free cooling in data centres are calculated. • The potential of TES integration in data centres is evaluated. • The implementation of TES to store the ambient air cold is not recommended. • TES is feasible if combined with redundant chillers and off-peak electricity price. • The cooling electricity cost is being reduced up to 51%, depending on the location

Electricity savings from implementation of minimum energy efficiency standard for TVs in Malaysia

Energy Technology Data Exchange (ETDEWEB)

Varman, M.; Masjuki, H.H.; Mahlia, T.M.I. [University of Malaya, Kuala Lumpur (Malaysia). Department of Mechanical Engineering

2005-06-01

The popularization of 24 h pay-TV, interactive video games, web-TV, VCD and DVD in Malaysia are poised to have a large impact on overall TV electricity consumption in the country. With the increasing of overall TV energy consumption, energy efficiency standards are one of highly effective policies for decreasing electricity consumption in the residential sector. Energy efficiency standards are also capable of reducing consumer's electricity bill and contribute towards positive environmental impacts. This paper attempts to predict the amount of energy that can be saved in the residential sector by implementing minimum energy efficiency standard for television sets in Malaysia. Over the past 30 years, television ownership in Malaysian residents has increased from 186,036 units in 1970 to 2,741,640 units in 1991. This figure is expected to reach 6,201,316 units in the year 2010. Hence, efficiency improvement for this appliance will have a significant impact on the future of electricity consumption in this country. (author)

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

Graphene oxide-mediated electrochemistry of glucose oxidase on glassy carbon electrodes.

Science.gov (United States)

Castrignanò, Silvia; Valetti, Francesca; Gilardi, Gianfranco; Sadeghi, Sheila J

2016-01-01

Glucose oxidase (GOD) was immobilized on glassy carbon electrodes in the presence of graphene oxide (GO) as a model system for the interaction between GO and biological molecules. Lyotropic properties of didodecyldimethylammonium bromide (DDAB) were used to stabilize the enzymatic layer on the electrode surface resulting in a markedly improved electrochemical response of the immobilized GOD. Transmission electron microscopy images of the GO with DDAB confirmed the distribution of the GO in a two-dimensional manner as a foil-like material. Although it is known that glassy carbon surfaces are not ideal for hydrogen peroxide detection, successful chronoamperometric titrations of the GOD in the presence of GO with β-d-glucose were performed on glassy carbon electrodes, whereas no current response was detected upon β-d-glucose addition in the absence of GO. The GOD-DDAB-GO system displayed a high turnover efficiency and substrate affinity as a glucose biosensor. The simplicity and ease of the electrode preparation procedure of this GO/DDAB system make it a good candidate for immobilizing other biomolecules for fabrication of amperometric biosensors. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

Minimum Energy Control of 2D Positive Continuous-Discrete Linear Systems

Directory of Open Access Journals (Sweden)

Kaczorek Tadeusz

2014-09-01

Full Text Available The minimum energy control problem for the 2D positive continuous-discrete linear systems is formulated and solved. Necessary and sufficient conditions for the reachability at the point of the systems are given. Sufficient conditions for the existence of solution to the problem are established. It is shown that if the system is reachable then there exists an optimal input that steers the state from zero boundary conditions to given final state and minimizing the performance index for only one step (q = 1. A procedure for solving of the problem is proposed and illustrated by a numerical example.

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

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.

Determination of minimum impact parameter by modified touching spheres schemes for intermediate energy Coulomb excitation experiments

International Nuclear Information System (INIS)

Kumar, Rajiv; Sharma, Shagun; Singh, Pradeep; Kharab, Rajesh

2016-01-01

The energy-independent touching spheres schemes commonly used for the determination of the safe minimum value of the impact parameter for Coulomb excitation experiments are modified through the inclusion of an energy-dependent term. The touching spheres+3fm scheme after modification emerges out to be the best one while touching spheres+4fm scheme is found to be better in its unmodified form. (orig.)

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

How mechanical behavior of glassy polymers enables us to characterize melt deformation: elastic yielding in glassy state after melt stretching?

Science.gov (United States)

Wang, Shi-Qing; Zhao, Zhichen; Tsige, Mesfin; Zheng, Yexin

Fast melt deformation well above the glass transition temperature Tg is known to produce elastic stress in an entangled polymer due to the chain entropy loss at the length scale of the network mesh size. Here chains of high molecular weight are assumed to form an entanglement network so that such a polymer behaves transiently like vulcanized rubber capable of affine deformation. We consider quenching a melt-deformed glassy polymer to well below Tg to preserve the elastic stress. Upon heating such a sample to Tg, the sample can return to the shape it took before melt deformation. This is the basic principle behind the design of all polymer-based shape-memory materials. This work presents intriguing evidence based on both experiment and computer simulation that the chain network, deformed well above Tg, can drive the glassy polymer to undergo elastic yielding. Our experimental systems include polystyrene, poly(methyl methacrylate) and polycarbonate; the molecular dynamics simulation is based on Kremer-Grest bead-spring model. National Science Foundation (DMR-1444859 and DMR-1609977).

SUPERNOVA SHOCK-WAVE-INDUCED CO-FORMATION OF GLASSY CARBON AND NANODIAMOND

International Nuclear Information System (INIS)

Stroud, Rhonda M.; Chisholm, Matthew F.; Heck, Philipp R.; Alexander, Conel M. O'D.; Nittler, Larry R.

2011-01-01

Nanodiamond (ND) was the first extrasolar dust phase to be identified in meteorites. However, the 2 nm average size of the NDs precludes isotopic analysis of individual particles, and thus their origin(s) remains controversial. Using electron microscopy with subnanometer resolution, we show that ND separates from the Allende and Murchison meteorites are actually a two-phase mixture of ND and glassy carbon. This phase mixture is likely the product of supernova shock-wave transformation of pre-formed organics in the interstellar medium (ISM). The glassy carbon-ND mixture is also a plausible contributor to the 2175 A extinction feature in the diffuse ISM.

Development and application of a free energy force field for all atom protein folding

International Nuclear Information System (INIS)

Verma, A.

2007-11-01

Proteins are the workhorses of all cellular life. They constitute the building blocks and the machinery of all cells and typically function in specific three-dimensional conformations into which each protein folds. Currently over one million protein sequences are known, compared to about 40,000 structures deposited in the Protein Data Bank (the world-wide database of protein structures). Reliable theoretical methods for protein structure prediction could help to reduce the gap between sequence and structural databases and elucidate the biological information in structurally unresolved sequences. In this thesis we explore an approach for protein structure prediction and folding that is based on the Anfinsen's hypothesis that most proteins in their native state are in thermodynamic equilibrium with their environment. We have developed a free energy forcefield (PFF02) that locates the native conformation of many proteins from all structural classes at the global minimum of the free-energy model. We have validated the forcefield against a large decoy set (Rosetta). The average root mean square deviation (RMSD) for the lowest energy structure for the 32 proteins of the decoy set was only 2.14 Aa from the experimental conformation. We have successfully implemented and used stochastic optimization methods, such as the basin hopping technique and evolutionary algorithms for all atom protein structure prediction. The evolutionary algorithm performs exceptionally well on large supercomputational architectures, such as BlueGene and MareNostrum. Using the PFF02 forcefield, we were able to fold 13 proteins (12-56 amino acids), which include helix, sheet and mixed secondary structure. On average the predicted structure of these proteins deviated from their experimental conformation by only 2.89 Aa RMSD. (orig.)

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.

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.

Alternative Energy: A Guide to Free Information for Educators.

Science.gov (United States)

White, Janet A.

This guide was compiled to help teachers and students locate free educational materials (both lessons and nontechnical background references) on renewable energy resources and energy conservation. The 214 entries are arranged by these topic areas: (1) energy efficiency and renewables; (2) biomass; (3) hydropower; (4) solar thermal energy; (5)…

Electrochemical pre anodization of glassy carbon electrode and application to determine chloramphenicol

International Nuclear Information System (INIS)

Truc, Nguyen Minh; Mortensen, John; Anh, Nguyen Ba Hoai

2008-01-01

This paper suggested a method to enhance the performance of carbon electrodes for the determination of chloramphenicol (CAP). The sensitivity and the reproducibility of the carbon electrodes could be enhanced easily by electrochemical pretreatment. Some kinds of carbon material were studied including glassy carbon, graphite carbon and pyrolytic carbon. Numerous kinds of supporting electrolyte have been tried. For glassy carbon electrode, the acidic solution, H 2 SO 4 5 mM, resulted in best performance at pretreated voltage of +2.1V (vs. Ag/ AgCl) in duration of 250 second. However, for graphite and pyrolytic carbon electrodes, the phosphate buffer solution pH 6.0 gave the best performance at +1.7V (vs. Ag/ AgCl) in duration of 20 seconds. The detection limit could be at very low concentration of CAP: 0.8 ng/ ml for glassy carbon electrode, 3.5 ng/ ml for graphite carbon electrode. The method was successful applied to aqua-agriculture water sample and milk sample with simple extraction as well as direct ointment sample analysis. (author)

Permeation of Mixed Penetrants through Glassy Polymer Membranes.

Science.gov (United States)

1985-03-15

and LOPE. Also, ESCA was used in conjunction with plasma etching to determine the effects of the gas phase fluorine concentration and fluorination...at 35 3C. ARD-AISS5 65 PERMEATION OF MIXED PENETRANTS THROUGH GLASSY POLYMER 213 MENBRANES (U) NORTH CAROLINA STATE UNIV AT RALEIGH R T CHERN ET AL. 15

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.

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...

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.

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.

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.

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.

Potential minimum cost of electricity of superconducting coil tokamak power reactors

International Nuclear Information System (INIS)

Reid, R.L.; Peng, Y-K. M.

1989-01-01

The potential minimum cost of electricity (COE) for superconducting tokamak power reactors is estimated by increasing the physics (confinement, beta limit, bootstrap current fraction) and technology [neutral beam energy, toroidal field (TF) coil allowable stresses, divertor heat flux, superconducting coil critical field, critical temperature, and quench temperature rise] constraints far beyond those assumed for ITER until the point of diminishing returns is reached. A version of the TETRA systems code, calibrated with the ITER design and modified for power reactors, is used for this analysis, limiting this study to reactors with the same basic device configuration and costing algorithms as ITER. A minimum COE is reduced from >200 to about 80 mill/kWh when the allowable design constraints are raised to 2 times those of ITER. At 4 times the ITER allowables, a minimum COE of about 60 mill/kWh is obtained. The corresponding tokamak has a major radius of approximately 4 m, a plasma current close to 10 MA, an aspect ratio of 4, a confinement H- factor ≤3, a beta limit of approximately 2 times the first stability regime, a divertor heat flux of about 20 MW/m 2 , a Β max ≤ 18 T, and a TF coil average current density about 3 times that of ITER. The design constraints that bound the minimum COE are the allowable stresses in the TF coil, the neutral beam energy, and the 99% bootstrap current (essentially free current drive). 14 refs., 4 figs., 2 tabs

Magnetic flux conversion and relaxation toward a minimum-energy state in S-1 spheromak plasmas

International Nuclear Information System (INIS)

Janos, A.

1985-09-01

S-1 Spheromak currents and magnetic fluxes have been measured with Rogowski coils and flux loops external to the plasma. Toroidal plasma currents up to 350 kA and spheromak configuration lifetimes over 1.0 msec have been achieved at moderate power levels. The plasma formation in the S-1 Spheromak device is based on an inductive transfer of poloidal and toroidal magnetic flux from a toroidal ''flux core'' to the plasma. Formation is programmed to guide the configuration into a force-free, minimum-energy Taylor state. Properly detailed programming of the formation process is found not to be essential since plasmas adjust themselves during formation to a final equilibrium near the Taylor state. After formation, if the plasma evolves away from the stable state, then distinct relaxation oscillation events occur which restore the configuration to that stable state. The relaxation process involves reconnection of magnetic field lines, and conversion of poloidal to toroidal magnetic flux (and vice versa) has been observed and documented. The scaling of toroidal plasma current and toroidal magnetic flux in the plasma with externally applied currents is consistent with the establishment of a Taylor state after formation. In addition, the magnetic helicity is proportional to that injected from the flux core, independent of how that helicity is generated

Effects of nymphal diet and adult feeding on allocation of resources to glassy-winged sharpshooter egg production

Science.gov (United States)

The glassy-winged sharpshooter is an invasive insect capable of transmitting the bacterial pathogen Xylella fastidiosa. Pre-oviposition periods of laboratory reared glassy-winged sharpshooters are variable. Here, two questions were addressed: does nymphal diet affect pre-oviposition period and how d...

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.

Pseudobinary glassy compositions (AsSex)1-y(AsTex)y

International Nuclear Information System (INIS)

El Mously, M.K.; El Dem, M.B.

1987-09-01

The ternery glassy composition of the general formula (AsSe x ) 1-y (AsTe x ) y can be considered as a pseudobinary system at x=1, 3/2 and 5/2 and 0 ≤ y ≤ 1. The results of DTA, electrical conductivity measurements, density of such glasses as well as the X-ray diffraction of the crystallized samples have been used to confirm this point of view and to explain the presence of new phases not shown in the simple binary systems As-Se and As-Te. The possibility of transformation of the glassy network from partially polymerized state MCN (molecular cluster network) to completely polymerized state CRN (continuous random network) by mixing two structural units was also discussed. (author). 12 refs, 7 figs, 2 tabs

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.

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.

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

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.

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...

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

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

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.

Low energy quasi free scattering on nuclear surface

Energy Technology Data Exchange (ETDEWEB)

Shiyuan, S.

1983-05-01

The result of RGM calculation of low energy /sup 3/He(n, n)/sup 3/ He total elastic cross section does not agree well with experimental data for E/sub n/<1 MeV. This discrepancy can be improved by assuming lwo energy quasi-free scattering of particles beyond the nuclear surface.

Ice cloud processing of ultra-viscous/glassy aerosol particles leads to enhanced ice nucleation ability

Directory of Open Access Journals (Sweden)

R. Wagner

2012-09-01

Full Text Available The ice nucleation potential of airborne glassy aqueous aerosol particles has been investigated by controlled expansion cooling cycles in the AIDA aerosol and cloud chamber of the Karlsruhe Institute of Technology at temperatures between 247 and 216 K. Four different solutes were used as proxies for oxygenated organic matter found in the atmosphere: raffinose, 4-hydroxy-3-methoxy-DL-mandelic acid (HMMA, levoglucosan, and a multi-component mixture of raffinose with five dicarboxylic acids and ammonium sulphate. Similar to previous experiments with citric acid aerosols, all particles were found to nucleate ice heterogeneously before reaching the homogeneous freezing threshold provided that the freezing cycles were started well below the respective glass transition temperatures of the compounds; this is discussed in detail in a separate article. In this contribution, we identify a further mechanism by which glassy aerosols can promote ice nucleation below the homogeneous freezing limit. If the glassy aerosol particles are probed in freezing cycles started only a few degrees below their respective glass transition temperatures, they enter the liquid regime of the state diagram upon increasing relative humidity (moisture-induced glass-to-liquid transition before being able to act as heterogeneous ice nuclei. Ice formation then only occurs by homogeneous freezing at elevated supersaturation levels. When ice forms the remaining solution freeze concentrates and re-vitrifies. If these ice cloud processed glassy aerosol particles are then probed in a second freezing cycle at the same temperature, they catalyse ice formation at a supersaturation threshold between 5 and 30% with respect to ice. By analogy with the enhanced ice nucleation ability of insoluble ice nuclei like mineral dusts after they nucleate ice once, we refer to this phenomenon as pre-activation. We propose a number of possible explanations for why glassy aerosol particles that have re

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.

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.

Trapped electron decay by the thermally-assisted tunnelling to electron acceptors in glassy matrices. A computer simulation study

International Nuclear Information System (INIS)

Feret, B.; Bartczak, W.M.; Kroh, J.

1991-01-01

The Redi-Hopefield quantum mechanical model of the thermally-assisted electron transfer has been applied to simulate the decay of trapped electrons by tunnelling to electron acceptor molecules added to the glassy matrix. It was assumed that the electron energy levels in donors and acceptors are statistically distributed and the electron excess energy after transfer is dissipated in the medium by the electron-phonon coupling. The electron decay curves were obtained by the method of computer simulation. It was found that for a given medium there exists a certain preferred value of the electronic excess energy which can be effectively converted into the matrix vibrations. If the mismatch of the electron states on the donor and acceptor coincides with the ''resonance'' energy the overall kinetics of electron transfer is accelerated. (author)

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

Interfacial electron transfer of glucose oxidase on poly(glutamic acid)-modified glassy carbon electrode and glucose sensing.

Science.gov (United States)

Zhou, Xuechou; Tan, Bingcan; Zheng, Xinyu; Kong, Dexian; Li, Qinglu

2015-11-15

The interfacial electron transfer of glucose oxidase (GOx) on a poly(glutamic acid)-modified glassy carbon electrode (PGA/GCE) was investigated. The redox peaks measured for GOx and flavin adenine dinucleotide (FAD) are similar, and the anodic peak of GOx does not increase in the presence of glucose in a mediator-free solution. These indicate that the electroactivity of GOx is not the direct electron transfer (DET) between GOx and PGA/GCE and that the observed electroactivity of GOx is ascribed to free FAD that is released from GOx. However, efficient electron transfer occurred if an appropriate mediator was placed in solution, suggesting that GOx is active. The PGA/GCE-based biosensor showed wide linear response in the range of 0.5-5.5 mM with a low detection limit of 0.12 mM and high sensitivity and selectivity for measuring glucose. Copyright © 2015 Elsevier Inc. All rights reserved.

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

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

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

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...

Arbitrage-free valuation of energy derivatives

International Nuclear Information System (INIS)

Amin, K.; Ng, V.; Pirrong, C.

1999-01-01

This chapter focuses on techniques available for valuing energy-contingent claims and develops an arbitrage-free framework to value energy derivatives. The relationship between the spot, forward and futures prices is explained. Option valuation with deterministic convenience yields is discussed using an extension of the Black (1976) framework, and details of the risk-neutral valuation of European options, and valuation of American and European-style options are given. Option valuations with stochastic convenience yields, the evolution of the term structure of convenience yield, and a tree approach to valuing American and other options are discussed. Applications and limitations of the models for pricing energy derivative products are considered. The stochastic differential equation for the futures prices when the convenience yields are stochastic is presented in an appendix

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

Is the Free Vacuum Energy Infinite?

International Nuclear Information System (INIS)

Shirazi, S. M.; Razmi, H.

2015-01-01

Considering the fundamental cutoff applied by the uncertainty relations’ limit on virtual particles’ frequency in the quantum vacuum, it is shown that the vacuum energy density is proportional to the inverse of the fourth power of the dimensional distance of the space under consideration and thus the corresponding vacuum energy automatically regularized to zero value for an infinitely large free space. This can be used in regularizing a number of unwanted infinities that happen in the Casimir effect, the cosmological constant problem, and so on without using already known mathematical (not so reasonable) techniques and tricks

Free-market approach to energy proposed in new study

International Nuclear Information System (INIS)

Anon.

1992-01-01

This paper reports that a free-market approach to energy use, intensified R and D and an emphasis on conservation and clean fuels such as natural gas can result in significant reductions in emissions of greenhouse gases, without any major new federal policy initiatives, according to a new study, An Alternative Energy Future, sponsored by Alliance to Save Energy, AGA and Solar Energy Industries Assn

Minimum energy path for the nucleation of misfit dislocations in Ge/Si(0 0 1) heteroepitaxy

International Nuclear Information System (INIS)

Trushin, O; Maras, E; Jónsson, H; Ala-Nissila, T; Stukowski, A; Granato, E; Ying, S C

2016-01-01

A possible mechanism for the formation of a 90° misfit dislocation at the Ge/Si(0 0 1) interface through homogeneous nucleation is identified from atomic scale calculations where a minimum energy path connecting the coherent epitaxial state and a final state with a 90° misfit dislocation is found using the nudged elastic band method. The initial path is generated using a repulsive bias activation procedure in a model system including 75 000 atoms. The energy along the path exhibits two maxima in the energy. The first maximum occurs as a 60° dislocation nucleates. The intermediate minimum corresponds to an extended 60° dislocation. The subsequent energy maximum occurs as a second 60° dislocation nucleates in a complementary, mirror glide plane, simultaneously starting from the surface and from the first 60° dislocation. The activation energy of the nucleation of the second dislocation is 30% lower than that of the first one showing that the formation of the second 60° dislocation is aided by the presence of the first one. The simulations represent a step towards unraveling the formation mechanism of 90° dislocations, an important issue in the design of growth procedures for strain released Ge overlayers on Si(1 0 0) surfaces, and more generally illustrate an approach that can be used to gain insight into the mechanism of complex nucleation paths of extended defects in solids. (paper)

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.

Simulation of the steady-state energy transfer in rigid bodies, with convective-radiative boundary conditions, employing a minimum principle

International Nuclear Information System (INIS)

Gama, R.M.S. da.

1992-08-01

The energy transfer phenomenon in a rigid and opaque body that exchanges energy, with the environment, by convection and by diffuse thermal radiation is studied. The considered phenomenon is described by a partial differential equation, subjected to (nonlinear) boundary conditions. A minimum principle, suitable for a large class of energy transfer problems is presented. Some particular cases are simulated. (author)

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...

Advanced Graphene-Based Binder-Free Electrodes for High-Performance Energy Storage.

Science.gov (United States)

Ji, Junyi; Li, Yang; Peng, Wenchao; Zhang, Guoliang; Zhang, Fengbao; Fan, Xiaobin

2015-09-23

The increasing demand for energy has triggered tremendous research effort for the development of high-performance and durable energy-storage devices. Advanced graphene-based electrodes with high electrical conductivity and ion accessibility can exhibit superior electrochemical performance in energy-storage devices. Among them, binder-free configurations can enhance the electron conductivity of the electrode, which leads to a higher capacity by avoiding the addition of non-conductive and inactive binders. Graphene, a 2D material, can be fabricated into a porous and flexible structure with an interconnected conductive network. Such a conductive structure is favorable for both electron and ion transport to the entire electrode surface. In this review, the main processes used to prepare binder-free graphene-based hybrids with high porosity and well-designed electron conductive networks are summarized. Then, the applications of free-standing binder-free graphene-based electrodes in energy-storage devices are discussed. Future research aspects with regard to overcoming the technological bottlenecks are also proposed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Minimum airflow reset of single-duct VAV terminal boxes

Science.gov (United States)

Cho, Young-Hum

Single duct Variable Air Volume (VAV) systems are currently the most widely used type of HVAC system in the United States. When installing such a system, it is critical to determine the minimum airflow set point of the terminal box, as an optimally selected set point will improve the level of thermal comfort and indoor air quality (IAQ) while at the same time lower overall energy costs. In principle, this minimum rate should be calculated according to the minimum ventilation requirement based on ASHRAE standard 62.1 and maximum heating load of the zone. Several factors must be carefully considered when calculating this minimum rate. Terminal boxes with conventional control sequences may result in occupant discomfort and energy waste. If the minimum rate of airflow is set too high, the AHUs will consume excess fan power, and the terminal boxes may cause significant simultaneous room heating and cooling. At the same time, a rate that is too low will result in poor air circulation and indoor air quality in the air-conditioned space. Currently, many scholars are investigating how to change the algorithm of the advanced VAV terminal box controller without retrofitting. Some of these controllers have been found to effectively improve thermal comfort, indoor air quality, and energy efficiency. However, minimum airflow set points have not yet been identified, nor has controller performance been verified in confirmed studies. In this study, control algorithms were developed that automatically identify and reset terminal box minimum airflow set points, thereby improving indoor air quality and thermal comfort levels, and reducing the overall rate of energy consumption. A theoretical analysis of the optimal minimum airflow and discharge air temperature was performed to identify the potential energy benefits of resetting the terminal box minimum airflow set points. Applicable control algorithms for calculating the ideal values for the minimum airflow reset were developed and

The energy landscape of glassy dynamics on the amorphous hafnium diboride surface

International Nuclear Information System (INIS)

Nguyen, Duc; Girolami, Gregory S.; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Lyding, Joseph; Gruebele, Martin

2014-01-01

Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB 2 glass surface, two-state hopping of 1–2 nm diameter cooperatively rearranging regions or “clusters” occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB 2 has a very high bulk glass transition temperature T g , and we observe no three-state hopping or sequential two-state hopping previously seen on lower T g glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how “mixed” features can show up in surface dynamics of glasses

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

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.

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.

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.)

Free-Free Transitions in the Presence of Laser Fields at Very Low Incident Electron Energy

Science.gov (United States)

Bhatia, A. K.; Sinha, Chandana

2010-01-01

We study the free-free transition in electron-hydrogenic systems in ground state in presence of an external laser field at very loud incident energies. The laser field is treated classically while the collision dynamics is treated quantum mechanically. The laser field is chosen to be monochromatic, linearly polarized and homogeneous. The incident electron is considered to be dressed by the laser in a nonperturbative manner by choosing a Volkov wave function for it. The scattering weave function for the electron is solved numerically by taking into account the effect of the electron exchange, short-range as well as of the long-range interactions to get the S and P wave phase shifts while for the higher angular momentum phase shifts the exchange approximation has only been considered. We calculate the laser assisted differential cross sections (LADCS) for the aforesaid free-free transition process for single photon absorption/emission. The laser intensity is chosen to be much less than the atomic field intensity. A strong suppression is noted in the LADCS as compared to the field free (FF) cross sections. Unlike the FF ones, the LADCS exhibit some oscillations having a distinct maximum at a low value of the scattering angle depending on the laser parameters as well as on the incident energies.

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.

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.

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.

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

Minimum Energy of a Prismatic Joint with out: Actuator: Application on RRP Robot

OpenAIRE

Tawiwat V.; Tosapolporn P.; Kedit J.

2009-01-01

This research proposes the state of art on how to control or find the trajectory paths of the RRP robot when the prismatic joint is malfunction. According to this situation, the minimum energy of the dynamic optimization is applied. The RRP robot or similar systems have been used in many areas such as fire fighter truck, laboratory equipment and military truck for example a rocket launcher. In order to keep on task that assigned, the trajectory paths must be computed. Here, the open loop cont...

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.

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...

Force-free field model of ball lightning

International Nuclear Information System (INIS)

Tsui, K.H.

2001-01-01

Due to the nature that the force-free magnetic field, whose current carried by the conducting plasma is everywhere parallel to the magnetic field it generates, is the minimum energy configuration under the constraint of magnetic helicity conservation, ball lightning is considered as a self-organized phenomenon with a plasma fireball immersed in a spherical force-free magnetic field. Since this field does not exert force on the plasma, the plasma pressure, by itself, is in equilibrium with the surrounding environment, and the force-free magnetic field can take on any value without affecting the plasma. Due to this second feature, singular solutions of the magnetic field that are otherwise excluded are allowed, which enable a large amount of energy to be stored to sustain the ball lightning. The singularity is truncated only by the physical limit of current density that a plasma can carry. Scaling the customary soccer-size fireball to larger dimensions could account for day and night sightings of luminous objects in the sky

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

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)

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

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.

Effect of glassy carbon properties on the electrochemical deposition of platinum nano-catalyst and its activity for methanol oxidation

Directory of Open Access Journals (Sweden)

SANJA TERZIC

2007-02-01

Full Text Available The effects of the properties of glassy carbon on the deposition of platinum particles and the electrocatalytic activity of platinum supported on glassy carbon (GC/Pt for methanol oxidation in alkaline and acidic solutions were studied. Platinum was potentiostatically deposited on two glassy carbon samples, thermally treated at different temperatures, which were either polished or anodicaly polarised in acid (GCOX-AC/Pt and in alkali (GCOX-AL/Pt. Anodic polarisation of glassy carbon, either in alkaline or acidic solution, enhances the activity of both types of GC/Pt electrodes for methanol oxidation. The activity of the catalysts follows the change in the properties of the glassy carbon support upon anodic treatment. The specific activity of the GCOX-AL/Pt electrode for this reaction in alkali is increased only a few times in comparison with the activity of the GC/Pt one. On the other hand, the specific activity of the GCOX-AC/Pt electrode for methanol oxidation in acid is about one order of magnitude higher than that of the GC/Pt electrode. The role of the substrate on the properties of catalyst is discussed in detail.

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.

Connection between NMR and electrical conductivity in glassy chalcogenide fast ionic conductors

International Nuclear Information System (INIS)

Kim, K.H.

1995-01-01

The work documented in this thesis follows the traditional order. In this chapter a general discussion of ionic conduction and of glassy materials are followed by a brief outline of the experimental techniques for the investigation of fast ionic conduction in glassy materials, including NMR and impedance spectroscopy techniques. A summary of the previous and present studies is presented in the last section of this introductory chapter. The details of the background theory and models are found in the Chapter II, followed by the description of the experimental details in Chapter III. Chapter IV of the thesis describes the experimental results and the analysis of the experimental observations followed by the conclusions in chapter V

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.

Temperature effects on the nuclear symmetry energy and symmetry free energy with an isospin and momentum dependent interaction

International Nuclear Information System (INIS)

Xu, Jun; Ma, Hong-Ru; Chen, Lie-Wen; Li, Bao-An

2007-01-01

Within a self-consistent thermal model using an isospin and momentum dependent interaction (MDI) constrained by the isospin diffusion data in heavy-ion collisions, we investigate the temperature dependence of the symmetry energy E sym (ρ,T) and symmetry free energy F sym (ρ,T) for hot, isospin asymmetric nuclear matter. It is shown that the symmetry energy E sym (ρ,T) generally decreases with increasing temperature while the symmetry free energy F sym (ρ,T) exhibits opposite temperature dependence. The decrement of the symmetry energy with temperature is essentially due to the decrement of the potential energy part of the symmetry energy with temperature. The difference between the symmetry energy and symmetry free energy is found to be quite small around the saturation density of nuclear matter. While at very low densities, they differ significantly from each other. In comparison with the experimental data of temperature dependent symmetry energy extracted from the isotopic scaling analysis of intermediate mass fragments (IMF's) in heavy-ion collisions, the resulting density and temperature dependent symmetry energy E sym (ρ,T) is then used to estimate the average freeze-out density of the IMF's

Orbital physics in sulfur spinels: ordered, liquid and glassy ground states

International Nuclear Information System (INIS)

Buettgen, N; Hemberger, J; Fritsch, V; Krimmel, A; Muecksch, M; Nidda, H-A Krug von; Lunkenheimer, P; Fichtl, R; Tsurkan, V; Loidl, A

2004-01-01

Measurements of magnetization M(T, H), heat capacity C(T), NMR lineshift K(T) and linewidth Δ(T), neutron scattering S(Q, ω, T) and broadband dielectric spectroscopy ε(ω, T) provide experimental evidence of the different orbital ground states in the cubic sulfur spinels under investigation. In all compounds, the tetrahedrally coordinated Jahn-Teller ions Fe 2+ are characterized by a degeneracy of the orbital degrees of freedom. Particularly, we found a long-range orbital ordering in polycrystalline (PC) FeCr 2 S 4 , and a glassy freezing of the orbital degrees of freedom in FeCr 2 S 4 (single crystals) (SCs). In contrast, FeSc 2 S 4 belongs to the rare class of spin-orbital liquids, where quantum fluctuations accompanying the glassy freezing of the orbitals suppress long-range magnetic order

Glassy behavior in the layered perovskites La2−xSrxCoO4(1.1≤x≤1.3)

International Nuclear Information System (INIS)

Mukherjee, S.; Mukherjee, Rajarshi; Banerjee, S.; Ranganathan, R.; Kumar, Uday

2012-01-01

The glassy behavior of the phase segregated state in the layered cobaltite La 2−x Sr x CoO 4 has been studied. The role of the inter-cluster interactions as well as the disordered spins at the paramagnetic–ferromagnetic interface, behind the observed glassy behavior have been investigated. The disordered spins at the interface appear to be strongly pinned, and they contribute little to the observed glassy behavior. On the other hand, the inter-cluster interactions play the key role. Both the Co 4+ and Co 3+ ions are in the intermediate spin state. - Highlights: ► Phase segregated state of cobaltite La 2−x Sr x CoO 4 for (1.1≤x≤1.3) to find the origin of the observed glassy behavior. ► Result of the frequency dependent ac susceptibility measurement excludes the possibility of any spin glass phase, hints strong inter-cluster interactions. ► Relaxation experiments confirm the system to be a collection of clusters with two preferred sizes. ► The glassy behavior originates from strong inter-cluster interactions.

Generation of fine hydromagmatic ash by growth and disintegration of glassy rinds

Science.gov (United States)

Mastin, L.G.

2007-01-01

The deposits of mafic hydromagmatic eruptions are more fine grained and variable in vesicularity than dry magmatic deposits. Blocky, equant shapes of many hydromagmatic clasts also contrast with droplet, thread, and bubble wall morphology of dry magmatic fragments. Small (disintegration of glassy rinds on pyroclast surfaces as they deform within turbulent flows. This process, termed "turbulent shedding", may occur during the expansion phase of vapor explosions or during turbulent but nonexplosive mixing of magma with water, steam, or water sprays. The occurrence of turbulent shedding and the resulting fragment sizes depend on the timescale for rind growth and the timescale between disturbances that remove or disintegrate glassy rinds. Turbulent shedding is directly observable in some small littoral jets at Kilauea. Calculations suggest that, in the presence of liquid water or water sprays, glassy rinds having a thickness of microns to millimeters should form in milliseconds to seconds. This is similar to the timescale between turbulent velocity fluctuations that can shred lava globules and remove such rinds. The fraction of a deposit consisting of fine ash should increase with the duration of this process: Large-scale Surtseyan jets generate hundreds or thousands of shedding events; bubble bursts or tephra jets at Kilauea's coast may produce only a few.

Protection of nuclear graphite toward fluoride molten salt by glassy carbon deposit

International Nuclear Information System (INIS)

Bernardet, V.; Gomes, S.; Delpeux, S.; Dubois, M.; Guerin, K.; Avignant, D.; Renaudin, G.; Duclaux, L.

2009-01-01

Molten salt reactor represents one of the promising future Generation IV nuclear reactors families where the fuel, a liquid molten fluoride salt, is circulating through the graphite reactor core. The interactions between nuclear graphite and fluoride molten salt and also the graphite surface protection were investigated in this paper by powder X-ray diffraction, micro-Raman spectroscopy and scanning electron microscopy coupled with X-ray microanalysis. Nuclear graphite discs were covered by two kinds of protection deposit: a glassy carbon coating and a double coating of pyrolitic carbon/glassy carbon. Different behaviours have been highlighted according to the presence and the nature of the coated protection film. Intercalation of molten salt between the graphite layers did not occur. Nevertheless the molten salt adhered more or less to the surface of the graphite disc, filled more or less the graphite surface porosity and perturbed more or less the graphite stacking order at the disc surface. The behaviour of unprotected graphite was far to be satisfactory after two days of immersion of graphite in molten salt at 500 deg. C. The best protection of the graphite disc surface, with the maximum of inertness towards molten salt, has been obtained with the double coating of pyrolitic carbon/glassy carbon

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.

Electrocatalytic Determination of Isoniazid by a Glassy Carbon Electrode Modified with Poly (Eriochrome Black T)

OpenAIRE

Karim Asadpour-Zeynali; Venus Baghalabadi

2017-01-01

In this work poly eriochrome black T (EBT) was electrochemically synthesized on the glassy carbon electrode as electrode modifier. On the modified electrode, voltammetric behavior of isoniazid (INH) was investigated. The poly (EBT)-modified glassy carbon electrode has excellent electrocatalytic ability for the electrooxidation of isoniazid. This fact was appeared as a reduced overpotential of INH oxidation in a wide operational pH range from 2 to 13. It has been found that the catalytic peak ...

Electrochemical Determination of Caffeine Content in Ethiopian Coffee Samples Using Lignin Modified Glassy Carbon Electrode

OpenAIRE

Amare, Meareg; Aklog, Senait

2017-01-01

Lignin film was deposited at the surface of glassy carbon electrode potentiostatically. In contrast to the unmodified glassy carbon electrode, an oxidative peak with an improved current and overpotential for caffeine at modified electrode showed catalytic activity of the modifier towards oxidation of caffeine. Linear dependence of peak current on caffeine concentration in the range 6 ? 10?6 to 100 ? 10?6?mol?L?1 with determination coefficient and method detection limit (LoD = 3?s/slope) of 0....

Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections

International Nuclear Information System (INIS)

Choe, G.S.; Cheng, C.Z.

2002-01-01

In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

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

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.

An anomalous X-ray scattering study on glassy superionic conductor (As2Se3)1-x(CuI) x using a third-generation synchrotron radiation facility

International Nuclear Information System (INIS)

Usuki, T.; Hosokawa, S.; Berar, J.-F.

2005-01-01

Anomalous X-ray scattering experiments on glassy superionic conductor (As 2 Se 3 ) 0.4 (CuI) 0.6 were performed at energies close to the As, Se, and Cu K edges using a new detecting system and a third-generation synchrotron radiation facility. The detecting system was composed of a graphite-crystal energy-analyzer and a NaI(Tl) detector on a 40-cm-long arm. The overall energy resolution was about 60 eV, which can discriminate the elastic signal from the fluorescence and Compton contributions, and a sufficient number of scattered X-ray photons were acquired within a reasonable data collection time. The differential structure factors, Δ i S(Q), were obtained from the detailed analyses, indicating that Δ As S(Q) and Δ Se S(Q) are similar to those of glassy As 2 Se 3 except at the prepeak position, and Δ Cu S(Q) that in liquid CuI. From these findings, it can be concluded that a pseudo-binary mixture of the As 2 Se 3 network matrix and CuI-related conduction pathways would be a good structural model for this superionic glass

Mechanical Properties for Reliability Analysis of Structures in Glassy Carbon

CERN Document Server

Garion, Cédric

2014-01-01

Despite its good physical properties, the glassy carbon material is not widely used, especially for structural applications. Nevertheless, its transparency to particles and temperature resistance are interesting properties for the applications to vacuum chambers and components in high energy physics. For example, it has been proposed for fast shutter valve in particle accelerator [1] [2]. The mechanical properties have to be carefully determined to assess the reliability of structures in such a material. In this paper, mechanical tests have been carried out to determine the elastic parameters, the strength and toughness on commercial grades. A statistical approach, based on the Weibull’s distribution, is used to characterize the material both in tension and compression. The results are compared to the literature and the difference of properties for these two loading cases is shown. Based on a Finite Element analysis, a statistical approach is applied to define the reliability of a structural component in gl...

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

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.

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)

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.

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.

Verification of the Taylor (minimum energy) state in the S-1 Spheromak

International Nuclear Information System (INIS)

Hart, G.W.; Janos, A.; Meyerhofer, D.D.; Yamada, M.

1985-09-01

Experimental measurements of the equilibrium in the S-1 Spheromak by use of magnetic probes inside the plasma show that the final magnetic equilibrium is one which has relaxed close to the Taylor (minimum-energy) state, even though the plasma is far from that state during formation. The comparison is made by calculating the two-dimensional μ profile of the plasma from the probe data, where μ is defined as μ 0 j/sub parallel//B. Measurements using a triple Langmuir probe provide evidence to support the conclusion that the pressure gradients in the relaxed state are confined to the edge region of the plasma

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.

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.)

Relook on fitting of viscosity with undercooling of glassy liquids

Indian Academy of Sciences (India)

Department of Materials Science and Engineering, Indian Institute of Technology, Kanpur ... The present approach is on the modification of viscosity fitting of undercooled liquid as a function of ... behaviour of glassy alloys and organic and ionic compounds ...... the present method is applied to calculate the analytical solu-.

Energy efficient structure-free data aggregation and delivery in WSN

Directory of Open Access Journals (Sweden)

Prabhudutta Mohanty

2016-11-01

Full Text Available In Wireless Sensor Networks (WSNs, the energy consumption due to the sensed data transmission is more than processing data locally within the sensor node. The data aggregation is one of the techniques to conserve energy by eliminating the redundant data transmission in dense WSNs. In this paper, we propose an energy efficient structure-free data aggregation and delivery (ESDAD protocol, which aggregates the redundant data in the intermediate nodes. In the proposed protocol, waiting time for packets at each intermediate node is calculated very sensibly so that data can be aggregated efficiently in the routing path. The sensed data packets are transmitted judicially to the aggregation point for data aggregation. The ESDAD protocol computes a cost function for structure-free, next-hop node selection and performs near source data aggregation. The buffer of each node is partitioned to maintain different types of flows for fair and efficient data delivery. The transmission rates of the sources and intermediate nodes are adjusted during congestion. The performance of the proposed protocol is evaluated through extensive simulations. The simulation results reveal that it outperforms the existing structure-free protocols in terms of energy efficiency, reliability and on-time delivery ratio.

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.

A nanoscale characterisation of extended defects in glassy-like As2Se3 semiconductors with PAL technique

International Nuclear Information System (INIS)

Shpotyuk, O.; Kovalskiy, A.; Filipecki, J.; Hyla, M.; Kozdras, A.

2003-01-01

A meaningful interpretation of positron lifetime characteristics for glassy-like g-As 2 Se 3 is developed taking into account calculations of Jensen et al. (J. Non-Cryst. Solids 170 (1994) 57) for positrons trapped by free-volume extended defects in orthorhombic As 2 Se 3 and void volume distribution for 146-atoms layer-biased model of amorphous As 2 Se 3 presented by Popescu (J. Non-Cryst. Solids 35-36 (1980) 549). The obtained results are compared for samples having different thermal pre-history. Two groups of experimental results with close lifetime characteristics are distinguished for each of the investigated samples. This feature is explained in terms of average positron lifetime by applying two-state positron trapping model for mathematical treatment of the obtained spectra

Electrical resistivity in Zr48Nb8Cu12Fe8Be24 glassy and crystallized alloys

Science.gov (United States)

Bai, H. Y.; Tong, C. Z.; Zheng, P.

2004-02-01

The electrical resistivity of Zr48Nb8Cu12Fe8Be24 bulk metallic glassy and crystallized alloys in the temperature range of 4.2-293 K is investigated. It is found that the resistivity in glassy and crystallized states shows opposite temperature coefficients. For the metallic glass, the resistivity shows a negative logarithmic dependence at temperatures below 16 K, whereas it has more normal behavior for the crystallized alloy. At higher temperatures, the resistivity in both glassy and crystallized alloys shows dependence upon both T and T2, but the signs of the T and T2 terms are opposite. The results are interpreted in terms of scattering from two-level tunneling states in glasses and the generalized Ziman diffraction model.

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.

Electrografting of diazonium-functionalized polyoxometalates: synthesis, immobilisation and electron-transfer characterisation from glassy carbon.

Science.gov (United States)

Rinfray, Corentin; Izzet, Guillaume; Pinson, Jean; Gam Derouich, Sarra; Ganem, Jean-Jacques; Combellas, Catherine; Kanoufi, Frédéric; Proust, Anna

2013-10-04

Polyoxometalates (POMs) are attractive candidates for the rational design of multi-level charge-storage materials because they display reversible multi-step reduction processes in a narrow range of potentials. The functionalization of POMs allows for their integration in hybrid complementary metal oxide semiconductor (CMOS)/molecular devices, provided that fine control of their immobilisation on various substrates can be achieved. Owing to the wide applicability of the diazonium route to surface modification, a functionalized Keggin-type POM [PW11 O39 {Ge(p-C6 H4 -CC-C6 H4 -${{\\rm N}{{+\\hfill \\atop 2\\hfill}}}$)}](3-) bearing a pending diazonium group was prepared and subsequently covalently anchored onto a glassy carbon electrode. Electron transfer with the immobilised POM was thoroughly investigated and compared to that of the free POM in solution. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

Electrochemical functionalization of glassy carbon electrode by reduction of diazonium cations in protic ionic liquid

International Nuclear Information System (INIS)

Shul, Galyna; Ruiz, Carlos Alberto Castro; Rochefort, Dominic; Brooksby, Paula A.; Bélanger, Daniel

2013-01-01

Protic ionic liquid based on 2-methoxypyridine and trifluoroacetic acid was used as electrolyte for the functionalization of a glassy carbon electrode surface by electrochemical reduction of in situ generated 4-chlorobenzene diazonium and 4-nitrobenzene diazonium cations. The diazonium cations were synthesized in an electrochemical cell by reaction of the corresponding amines with NaNO 2 dissolved in protic ionic liquid. The resulting electrografted organic layers exhibit similar properties to those layers obtained by the derivatization from isolated diazonium salts dissolved in protic ionic liquid. Functionalized glassy carbon electrode surfaces were characterized by cyclic voltammetry, Fourier transform infrared and X-ray photoelectron spectroscopies. Atomic force microscopy thickness measurements revealed that, in our experimental conditions, the use of protic ionic liquid led to the formation of film with a thickness of about 1.5 nm. It is also demonstrated that the nitrobenzene chemisorbed on glassy carbon electrode or dissolved in protic ionic liquid undergoes electrochemical conversion to hydroxyaminobenzene

Preference of small molecules for local minimum conformations when binding to proteins.

Directory of Open Access Journals (Sweden)

Qi Wang

2007-09-01

Full Text Available It is well known that small molecules (ligands do not necessarily adopt their lowest potential energy conformations when binding to proteins. Analyses of protein-bound ligand crystal structures have reportedly shown that many of them do not even adopt the conformations at local minima of their potential energy surfaces (local minimum conformations. The results of these analyses raise a concern regarding the validity of virtual screening methods that use ligands in local minimum conformations. Here we report a normal-mode-analysis (NMA study of 100 crystal structures of protein-bound ligands. Our data show that the energy minimization of a ligand alone does not automatically stop at a local minimum conformation if the minimum of the potential energy surface is shallow, thus leading to the folding of the ligand. Furthermore, our data show that all 100 ligand conformations in their protein-bound ligand crystal structures are nearly identical to their local minimum conformations obtained from NMA-monitored energy minimization, suggesting that ligands prefer to adopt local minimum conformations when binding to proteins. These results both support virtual screening methods that use ligands in local minimum conformations and caution about possible adverse effect of excessive energy minimization when generating a database of ligand conformations for virtual screening.

Voltammetric determination of bisphenol A in food package by a glassy carbon electrode modified with carboxylated multi-walled carbon nanotubes

International Nuclear Information System (INIS)

Li, J.; Kuang, D.; Feng, Y.; Zhang, F.; Liu, M.

2011-01-01

A highly sensitive and mercury-free method for determination of bisphenol A (BPA) was established using a glassy carbon electrode that was modified with carboxylated multi-walled carbon nanotubes. A sensitive oxidation peak is found at 550 mV in linear sweep voltammograms at pH 7. Based on this finding, trace levels of bisphenol A can be determined over a concentration range that is linear from 10 nM to 104 nM, the correlation coefficient being 0.9983, and the detection limit (S/N = 3) being 5.0 nM. The method was successfully applied to the determination of BPA in food package. (author)

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.

Some Recent Developments in Structure and Glassy Behavior of Proteins

Science.gov (United States)

Hu, Chin-Kun

2012-02-01

We have used ARVO developed by us to find that the ratio of volume and surface area of proteins in Protein Data Bank distributed in a very narrow region [1]. Such result is useful for the determination of protein 3D structures. It has been widely known that a spin glass model can be used to understand the slow relaxation behavior of a glass at low temperatures [2]. We have used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that polymer chains with neighboring monomers connected by rigid bonds can relax very slowly and show glassy behavior [3]. We have also found that native collagen fibrils show glassy behavior at room temperatures [4]. The results of [3] and [4] about the glassy behavior of polymers or proteins are useful for understanding the mechanism for a biological system to maintain in a non-equilibrium state, including the ancient seed [5], which can maintain in a non-equilibrium state for a very long time. (1) M.-C. Wu, M. S. Li, W.-J. Ma, M. Kouza, and C.-K. Hu, EPL, in press (2011); (2) C. Dasgupta, S.-K. Ma, and C.-K. Hu. Phys. Rev. B 20, 3837-3849 (1979); (3) W.-J. Ma and C.-K. Hu, J. Phys. Soc. Japan 79, 024005, 024006, 054001, and 104002 (2010), C.-K. Hu and W.-J. Ma, Prog. Theor. Phys. Supp. 184, 369 (2010); S. G. Gevorkian, A. E. Allahverdyan, D. S. Gevorgyan and C.-K. Hu, EPL 95, 23001 (2011); S. Sallon, et al. Science 320, 1464 (2008).

Applications for Energy Recovering Free Electron Lasers

Energy Technology Data Exchange (ETDEWEB)

George Neil

2007-08-01

The availability of high-power, high-brilliance sources of tunable photons from energy-recovered Free Electron Lasers is opening up whole new fields of application of accelerators in industry. This talk will review some of the ideas that are already being put into production, and some of the newer ideas that are still under development.

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.

Local thermal energy as a structural indicator in glasses

Science.gov (United States)

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-01

Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

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.

Prediction of free-volume-type correlations in glassy chalcogenides from positron annihilation lifetime measurements

International Nuclear Information System (INIS)

Shpotyuk, O.; Ingram, A.; Shpotyuk, M.; Filipecki, J.

2014-01-01

Highlights: • Decisive role of specific chemical environment in free-volume correlations in glass. • Realistic free volumes in As–S/Se glass are defined by newly modified τ 2 -R formula. • Overestimated void sizes in chalcogenide glass as compared with molecular polymers. - Abstract: A newly modified correlation equation between defect-related positron lifetime determined within two-state trapping model and radius of corresponding free-volume-type defects was proposed to describe compositional variations in atomic-deficient structure of covalent-bonded chalcogenides like binary As–S/Se glasses. Specific chemical environment of free-volume voids around neighboring network-forming polyhedrons was shown to play a decisive role in this correlation, leading to systematically enhanced volumes in comparison with typical molecular substrates, such as polymers

Prediction of free-volume-type correlations in glassy chalcogenides from positron annihilation lifetime measurements

Energy Technology Data Exchange (ETDEWEB)

Shpotyuk, O., E-mail: shpotyuk@novas.lviv.ua [Institute of Materials of SRC “Carat”, 212 Stryjska Str., Lviv 79031 (Ukraine); Institute of Physics of Jan Dlugosz University, 13/15 al. Armii Krajowej, Czestcochowa 42200 (Poland); Ingram, A. [Opole University of Technology, 75 Ozimska Str., Opole 45370 (Poland); Shpotyuk, M. [Institute of Materials of SRC “Carat”, 212 Stryjska Str., Lviv 79031 (Ukraine); Lviv Polytechnic National University, 12 Bandery Str., Lviv 79013 (Ukraine); Filipecki, J. [Institute of Physics of Jan Dlugosz University, 13/15 al. Armii Krajowej, Czestcochowa 42200 (Poland)

2014-11-01

Highlights: • Decisive role of specific chemical environment in free-volume correlations in glass. • Realistic free volumes in As–S/Se glass are defined by newly modified τ{sub 2}-R formula. • Overestimated void sizes in chalcogenide glass as compared with molecular polymers. - Abstract: A newly modified correlation equation between defect-related positron lifetime determined within two-state trapping model and radius of corresponding free-volume-type defects was proposed to describe compositional variations in atomic-deficient structure of covalent-bonded chalcogenides like binary As–S/Se glasses. Specific chemical environment of free-volume voids around neighboring network-forming polyhedrons was shown to play a decisive role in this correlation, leading to systematically enhanced volumes in comparison with typical molecular substrates, such as polymers.

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

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.

A study of nanostructured gold modified glassy carbon electrode for ...

Indian Academy of Sciences (India)

A nanostructured gold modified glassy carbon electrode (Aunano/GCE) was employed for the determination of trace chromium(VI). To prepare Aunano/GCE, the GCE was immersed into KAuCl4 solution and electrodeposition was conducted at the potential of -0.4 V (vs Ag/AgCl) for 600 s. Scanning electron microscopy ...

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.

Gold nanoparticles directly modified glassy carbon electrode for non-enzymatic detection of glucose

Energy Technology Data Exchange (ETDEWEB)

Chang, Gang; Shu, Honghui; Ji, Kai [Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Science and Engineering, Hubei University, No. 368 Youyi Avenue, Wuchang, Wuhan 430062 (China); Oyama, Munetaka [Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8520 (Japan); Liu, Xiong [Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Science and Engineering, Hubei University, No. 368 Youyi Avenue, Wuchang, Wuhan 430062 (China); He, Yunbin, E-mail: ybhe@hubu.edu.cn [Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Science and Engineering, Hubei University, No. 368 Youyi Avenue, Wuchang, Wuhan 430062 (China)

2014-01-01

This work describes controllable preparation of gold nanoparticles on glassy carbon electrodes by using the seed mediated growth method, which contains two steps, namely, nanoseeds attachment and nanocrystals growth. The size and the dispersion of gold nanoparticles grown on glassy carbon electrodes could be easily tuned through the growth time based on results of field-emission scanning electron microscopy. Excellent electrochemical catalytic characteristics for glucose oxidation were observed for the gold nanoparticles modified glassy carbon electrodes (AuNPs/GC), resulting from the extended active surface area provided by the dense gold nanoparticles attached. It exhibited a wide linear range from 0.1 mM to 25 mM with the sensitivity of 87.5 μA cm{sup −2} mM{sup −1} and low detection limit down to 0.05 mM for the sensing of glucose. The common interfering species such as chloride ion, ascorbic acid, uric acid and 4-acetamidophenol were verified having no interference effect on the detection of glucose. It is demonstrated that the seed mediated method is one of the facile approaches for fabricating Au nanoparticles modified substrates, which could work as one kind of promising electrode materials for the glucose nonenzymatic sensing.

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+)