Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid
2017-12-07
Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.
Sastre, Francisco; Moreno-Hilario, Elizabeth; Sotelo-Serna, Maria Guadalupe; Gil-Villegas, Alejandro
2018-02-01
The microcanonical-ensemble computer simulation method (MCE) is used to evaluate the perturbation terms Ai of the Helmholtz free energy of a square-well (SW) fluid. The MCE method offers a very efficient and accurate procedure for the determination of perturbation terms of discrete-potential systems such as the SW fluid and surpass the standard NVT canonical ensemble Monte Carlo method, allowing the calculation of the first six expansion terms. Results are presented for the case of a SW potential with attractive ranges 1.1 ≤ λ ≤ 1.8. Using semi-empirical representation of the MCE values for Ai, we also discuss the accuracy in the determination of the phase diagram of this system.
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
Matova, S.P.; Elfrink, R.; Vullers, R.J.M.; Schaijk, R. van
2011-01-01
In this paper we report an airflow energy harvester that combines a piezoelectric energy harvester with a Helmholtz resonator. The resonator converts airflow energy to air oscillations which in turn are converted into electrical energy by a piezoelectric harvester. Two Helmholtz resonators with
Acoustic energy harvesting using an electromechanical Helmholtz resonator.
Liu, Fei; Phipps, Alex; Horowitz, Stephen; Ngo, Khai; Cattafesta, Louis; Nishida, Toshikazu; Sheplak, Mark
2008-04-01
This paper presents the development of an acoustic energy harvester using an electromechanical Helmholtz resonator (EMHR). The EMHR consists of an orifice, cavity, and a piezoelectric diaphragm. Acoustic energy is converted to mechanical energy when sound incident on the orifice generates an oscillatory pressure in the cavity, which in turns causes the vibration of the diaphragm. The conversion of acoustic energy to electrical energy is achieved via piezoelectric transduction in the diaphragm of the EMHR. Moreover, the diaphragm is coupled with energy reclamation circuitry to increase the efficiency of the energy conversion. Lumped element modeling of the EMHR is used to provide physical insight into the coupled energy domain dynamics governing the energy reclamation process. The feasibility of acoustic energy reclamation using an EMHR is demonstrated in a plane wave tube for two power converter topologies. The first is comprised of only a rectifier, and the second uses a rectifier connected to a flyback converter to improve load matching. Experimental results indicate that approximately 30 mW of output power is harvested for an incident sound pressure level of 160 dB with a flyback converter. Such power level is sufficient to power a variety of low power electronic devices.
Matova, S P; Elfrink, R; Vullers, R J M; Van Schaijk, R
2011-01-01
In this paper we report an airflow energy harvester that combines a piezoelectric energy harvester with a Helmholtz resonator. The resonator converts airflow energy to air oscillations which in turn are converted into electrical energy by a piezoelectric harvester. Two Helmholtz resonators with adjustable resonance frequencies have been designed—one with a solid bottom and one with membrane on the bottom. The resonance frequencies of the resonators were matched to the complementing piezoelectric harvesters during harvesting. The aim of the presented work is a feasibility study on using packaged piezoelectric energy harvesters with Helmholtz resonators for airflow energy harvesting. The maximum energy we were able to obtain was 42.2 µW at 20 m s −1
Holm, Oeystein B.
2006-01-01
Norway has fallen behind in the development of district heating and use of solar energy compared to Sweden and Denmark. It is a myth that Norway has less hours of sun than its neighbours; southern and eastern Norway has equally good conditions as areas in Sweden and Denmark that have large solar collector installations used for district heating. Benefits of the solar energy technology are highlighted, especially environmental aspects (ml)
Free energy of the Lennard-Jones solid
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
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
Progress toward Kelvin-Helmholtz instabilities in a High-Energy-Density Plasma on the Nike laser
Harding, E. C.; Drake, R. P.; Gillespie, R. S.; Grosskopf, M. J.; Huntington, C. M.; Aglitskiy, Y.; Weaver, J. L.; Velikovich, A. L.; Plewa, T.; Dwarkadas, V. V.
2008-04-01
In the realm of high-energy-density (HED) plasmas, there exist three primary hydrodynamic instabilities of concern: Rayleigh-Taylor (RT), Richtmyer-Meshkov (RM), and Kelvin-Helmholtz (KH). Although the RT and the RM instabilities have been readily observed and diagnosed in the laboratory, the KH instability remains relatively unexplored in HED plasmas. Unlike the RT and RM instabilities, the KH instability is driven by a lifting force generated by a strong velocity gradient in a stratified fluid. Understanding the KH instability mechanism in HED plasmas will provide essential insight into oblique shock systems, jets, mass stripping, and detailed RT-spike development. In addition, our KH experiment will help provide the groundwork for future transition to turbulence experiments. We present 2D FLASH simulations and experimental data from our initial attempts to create a pure KH system using the Nike laser at the Naval Research Laboratory.
Ananthakrishnan, Palaniswamy
2012-11-01
The problem is of practical relevance in determining the motion response of multi-hull and air-cushion vehicles in high seas and in littoral waters. The linear inviscid problem without surface pressure has been well studied in the past. In the present work, the nonlinear wave-body interaction problem is solved using finite-difference methods based on boundary-fitted coordinates. The inviscid nonlinear problem is tackled using the mixed Eulerian-Lagrangian formulation and the solution of the incompressible Navier-Stokes equations governing the viscous problem using a fractional-step method. The pressure variation in the air cushion is modeled using the isentropic gas equation pVγ = Constant. Results show that viscosity and free-surface nonlinearity significantly affect the hydrodynamic force and the wave motion at the resonant Helmholtz frequency (at which the primary wave motion is the vertical oscillation of the mean surface in between the bodies). Air compressibility suppresses the Helmholtz oscillation and enhances the wave radiation. Work supported by the ONR under the grant N00014-98-1-0151.
De Kock, Liesbet
2016-04-01
In this analysis, the classical problem of Hermann von Helmholtz's (1821-1894) Kantianism is explored from a particular vantage point, that to my knowledge, has not received the attention it deserves notwithstanding its possible key role in disentangling Helmholtz's relation to Kant's critical project. More particularly, we will focus on Helmholtz's critical engagement with Kant's concept of intuition [Anschauung] and (the related issue of) his dissatisfaction with Kant's doctrinal dualism. In doing so, it soon becomes clear that both (i) crucially mediated Helmholtz's idiosyncratic appropriation and criticism of (certain aspects of) Kant's critical project, and (ii) can be considered as a common denominator in a variety of issues that are usually addressed separately under the general header of (the problem of) Helmholtz's Kantianism. The perspective offered in this analysis can not only shed interesting new light on some interpretive issues that have become commonplace in discussions on Helmholtz's Kantianism, but also offers a particular way of connecting seemingly unrelated dimensions of Helmholtz's engagement with Kant's critical project (e.g. Helmholtz's views on causality and space). Furthermore, it amounts to the rather surprising conclusion that Helmholtz's most drastic revision of Kant's project pertains to his assumption of free will as a formal condition of experience and knowledge. Copyright © 2015 Elsevier Ltd. All rights reserved.
Wolfgang Albrecht
2017-05-01
Full Text Available The Helmholtz Nano Facility (HNF is a state-of-the-art cleanroom facility. The cleanroom has ~1100 m2 with cleanroom classes of DIN ISO 1-3. HNF operates according to VDI DIN 2083, Good Manufacturing Practice (GMP and aquivalent to Semiconductor Industry Association (SIA standards. HNF is a user facility of Forschungszentrum Jülich and comprises a network of facilities, processes and systems for research, production and characterization of micro- and nanostructures. HNF meets the basic supply of micro- and nanostructures for nanoelectronics, fluidics. micromechanics, biology, neutron and energy science, etc.. The task of HNF is rapid progress in nanostructures and their technology, offering efficient access to infrastructure and equipment. HNF gives access to expertise and provides resources in production, synthesis, characterization and integration of structures, devices and circuits. HNF covers the range from basic research to application oriented research facilitating a broad variety of different materials and different sample sizes.
Okamoto, Kazuhisa; Nonaka, Chiho
2017-06-01
We construct a new relativistic viscous hydrodynamics code optimized in the Milne coordinates. We split the conservation equations into an ideal part and a viscous part, using the Strang spitting method. In the code a Riemann solver based on the two-shock approximation is utilized for the ideal part and the Piecewise Exact Solution (PES) method is applied for the viscous part. We check the validity of our numerical calculations by comparing analytical solutions, the viscous Bjorken's flow and the Israel-Stewart theory in Gubser flow regime. Using the code, we discuss possible development of the Kelvin-Helmholtz instability in high-energy heavy-ion collisions.
Free Energy in Introductory Physics
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…
SOCIAL EQUIVALENT OF FREE ENERGY
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.
Xiong Shiyun; Qi Weihong; Huang Baiyun; Wang Mingpu; Li Yejun
2010-01-01
The Debye model of Helmholtz free energy for bulk material is generalized to Gibbs free energy (GFE) model for nanomaterial, while a shape factor is introduced to characterize the shape effect on GFE. The structural transitions of Ti and Zr nanoparticles are predicted based on GFE. It is further found that GFE decreases with the shape factor and increases with decreasing of the particle size. The critical size of structural transformation for nanoparticles goes up as temperature increases in the absence of change in shape factor. For specified temperature, the critical size climbs up with the increase of shape factor. The present predictions agree well with experiment values.
Okamoto, Kazuhisa [Nagoya University, Department of Physics, Nagoya (Japan); Nonaka, Chiho [Nagoya University, Department of Physics, Nagoya (Japan); Nagoya University, Kobayashi-Maskawa Institute for the Origin of Particles and the Universe (KMI), Nagoya (Japan); Duke University, Department of Physics, Durham, NC (United States)
2017-06-15
We construct a new relativistic viscous hydrodynamics code optimized in the Milne coordinates. We split the conservation equations into an ideal part and a viscous part, using the Strang spitting method. In the code a Riemann solver based on the two-shock approximation is utilized for the ideal part and the Piecewise Exact Solution (PES) method is applied for the viscous part. We check the validity of our numerical calculations by comparing analytical solutions, the viscous Bjorken's flow and the Israel-Stewart theory in Gubser flow regime. Using the code, we discuss possible development of the Kelvin-Helmholtz instability in high-energy heavy-ion collisions. (orig.)
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)
Grain-boundary free energy in an assembly of elastic disks.
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.
Kelvin-Helmholtz instability in solar spicules
H Ebadi
2016-12-01
Full Text Available Magneto hydrodynamic waves, propagating along spicules, may become unstable and the expected instability is of Kelvin-Helmholtz type. Such instability can trigger the onset of wave turbulence leading to an effective plasma heating and particle acceleration. In present study, two-dimensional magneto hydrodynamic simulations performed on a Cartesian grid is presented in spicules with different densities, moving at various speeds depending on their environment. Simulations being applied in this study show the onset of Kelvin-Helmholtz type instability and transition to turbulent flow in spicules. Development of Kelvin-Helmholtz instability leads to momentum and energy transport, dissipation, and mixing of fluids. When magnetic fields are involved, field amplification is also possible to take place
Free energies of stable and metastable pores in lipid membranes under tension.
den Otter, Wouter K
2009-11-28
The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to obtain the Helmholtz free energy as a function of pore size for thermodynamically stable, metastable, and unstable pores, and the system-size dependence of these elongations is discussed. A link to the Gibbs free energy at constant tension, commonly known as the Litster model, is established by a Legendre transformation. The change of genus upon pore formation is exploited to estimate the saddle-splay modulus or Gaussian curvature modulus of the membrane leaflets. Details are provided of the simulation approach, which combines the potential of mean constraint force method with a reaction coordinate based on the local lipid density.
Christian, J M; McDonald, G S [Joule Physics Laboratory, School of Computing, Science and Engineering, Materials and Physics Research Centre, University of Salford, Salford M5 4WT (United Kingdom); Chamorro-Posada, P, E-mail: j.christian@salford.ac.u [Departamento de Teoria de la Senal y Comunicaciones e Ingenieria Telematica, Universidad de Valladolid, ETSI Telecomunicacion, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)
2010-02-26
We report, to the best of our knowledge, the first exact analytical algebraic solitons of a generalized cubic-quintic Helmholtz equation. This class of governing equation plays a key role in photonics modelling, allowing a full description of the propagation and interaction of broad scalar beams. New conservation laws are presented, and the recovery of paraxial results is discussed in detail. The stability properties of the new solitons are investigated by combining semi-analytical methods and computer simulations. In particular, new general stability regimes are reported for algebraic bright solitons.
Christian, J M; McDonald, G S; Chamorro-Posada, P
2010-01-01
We report, to the best of our knowledge, the first exact analytical algebraic solitons of a generalized cubic-quintic Helmholtz equation. This class of governing equation plays a key role in photonics modelling, allowing a full description of the propagation and interaction of broad scalar beams. New conservation laws are presented, and the recovery of paraxial results is discussed in detail. The stability properties of the new solitons are investigated by combining semi-analytical methods and computer simulations. In particular, new general stability regimes are reported for algebraic bright solitons.
Free energy of hydration of niobium oxide
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
Capillary and viscous perturbations to Helmholtz flows
Moore, M. R.; Ockendon, H.; Ockendon, J. R.; Oliver, J. M.
2014-01-01
Inspired by recent calculations by Thoraval et al. (Phys. Rev. Lett., vol. 108, 2012, p.Â 264506) relating to droplet impact, this paper presents an analysis of the perturbations to the free surface caused by small surface tension and viscosity in steady Helmholtz flows. In particular, we identify the regimes in which appreciable vorticity can be shed from the boundary layer to the bulk flow. © 2014 Cambridge University Press.
Capillary and viscous perturbations to Helmholtz flows
Moore, M. R.
2014-02-21
Inspired by recent calculations by Thoraval et al. (Phys. Rev. Lett., vol. 108, 2012, p.Â 264506) relating to droplet impact, this paper presents an analysis of the perturbations to the free surface caused by small surface tension and viscosity in steady Helmholtz flows. In particular, we identify the regimes in which appreciable vorticity can be shed from the boundary layer to the bulk flow. © 2014 Cambridge University Press.
Tsallis’ non-extensive free energy as a subjective value of an uncertain reward
Takahashi, Taiki
2009-03-01
Recent studies in neuroeconomics and econophysics revealed the importance of reward expectation in decision under uncertainty. Behavioral neuroeconomic studies have proposed that the unpredictability and the probability of an uncertain reward are distinctly encoded as entropy and a distorted probability weight, respectively, in the separate neural systems. However, previous behavioral economic and decision-theoretic models could not quantify reward-seeking and uncertainty aversion in a theoretically consistent manner. In this paper, we have: (i) proposed that generalized Helmholtz free energy in Tsallis’ non-extensive thermostatistics can be utilized to quantify a perceived value of an uncertain reward, and (ii) empirically examined the explanatory powers of the models. Future study directions in neuroeconomics and econophysics by utilizing the Tsallis’ free energy model are discussed.
Modern solvers for Helmholtz problems
Tang, Jok; Vuik, Kees
2017-01-01
This edited volume offers a state of the art overview of fast and robust solvers for the Helmholtz equation. The book consists of three parts: new developments and analysis in Helmholtz solvers, practical methods and implementations of Helmholtz solvers, and industrial applications. The Helmholtz equation appears in a wide range of science and engineering disciplines in which wave propagation is modeled. Examples are: seismic inversion, ultrasone medical imaging, sonar detection of submarines, waves in harbours and many more. The partial differential equation looks simple but is hard to solve. In order to approximate the solution of the problem numerical methods are needed. First a discretization is done. Various methods can be used: (high order) Finite Difference Method, Finite Element Method, Discontinuous Galerkin Method and Boundary Element Method. The resulting linear system is large, where the size of the problem increases with increasing frequency. Due to higher frequencies the seismic images need to b...
Microscopically derived free energy of dislocations
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
Another Look at Helmholtz's Model for the Gravitational Contraction of the Sun
Tort, A. C.; Nogarol, F.
2011-01-01
We take another look at the Helmholtz model for the gravitational contraction of the Sun. We show that there are two other pedagogically useful ways of rederiving Helmholtz's main results that make use of Gauss's law, the concept of gravitational field energy and the work-kinetic energy theorem. An account of the energy balance involved in the…
Uncertainty Quantification in Alchemical Free Energy Methods.
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.
Mechanism of active transport: free energy dissipation and free energy transduction.
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 ...
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.
Free Energy and Internal Combustion Engine Cycles
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.
Good Practices in Free-energy Calculations
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.
Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.
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
Can Hall effect trigger Kelvin-Helmholtz instability in sub-Alfvénic flows?
Pandey, B. P.
2018-05-01
In the Hall magnetohydrodynamics, the onset condition of the Kelvin-Helmholtz instability is solely determined by the Hall effect and is independent of the nature of shear flows. In addition, the physical mechanism behind the super- and sub-Alfvénic flows becoming unstable is quite different: the high-frequency right circularly polarized whistler becomes unstable in the super-Alfvénic flows whereas low-frequency, left circularly polarized ion-cyclotron wave becomes unstable in the presence of sub-Alfvénic shear flows. The growth rate of the Kelvin-Helmholtz instability in the super-Alfvénic case is higher than the corresponding ideal magnetohydrodynamic rate. In the sub-Alfvénic case, the Hall effect opens up a new, hitherto inaccessible (to the magnetohydrodynamics) channel through which the partially or fully ionized fluid can become Kelvin-Helmholtz unstable. The instability growth rate in this case is smaller than the super-Alfvénic case owing to the smaller free shear energy content of the flow. When the Hall term is somewhat smaller than the advection term in the induction equation, the Hall effect is also responsible for the appearance of a new overstable mode whose growth rate is smaller than the purely growing Kelvin-Helmholtz mode. On the other hand, when the Hall diffusion dominates the advection term, the growth rate of the instability depends only on the Alfvén -Mach number and is independent of the Hall diffusion coefficient. Further, the growth rate in this case linearly increases with the Alfvén frequency with smaller slope for sub-Alfvénic flows.
Brett, Walter
2014-07-21
In the presented work the Kelvin-Helmholtz-Instability in magnetohydrodynamic flows is analyzed with the methods of Multiple Scales. The concerned fluids are incompressible or have a varying density perpendicular to the vortex sheet, which is taken into account using a Boussinesq-Approximation and constant Brunt-Vaeisaelae-Frequencies. The Multiple Scale Analysis leads to nonlinear evolution equations for the amplitude of the perturbations. Special solutions to these equations are presented and the effects of the magnetic fields are discussed.
Free energy analysis of cell spreading.
McEvoy, Eóin; Deshpande, Vikram S; McGarry, Patrick
2017-10-01
In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading. Simulations suggest that cell spreading can be viewed as a competition between (i) decreasing cytoskeletal free energy due to strain induced assembly of cytoskeletal proteins into contractile SFs, and (ii) increasing elastic free energy due to stretching of the mechanically passive components of the cell. The computed minimum free energy spread area is shown to be lower for a cell on a compliant substrate than on a rigid substrate. Furthermore, a low substrate ligand density is found to limit cell spreading. The predicted dependence of cell spread area on substrate stiffness and ligand density is in agreement with the experiments of Engler et al. (2003). We also simulate the experiments of Théry et al. (2006), whereby initially circular cells deform and adhere to "V-shaped" and "Y-shaped" ligand patches. Analysis of a number of different spread states reveals that deformed configurations with the lowest free energy exhibit a SF distribution that corresponds to experimental observations, i.e. a high concentration of highly aligned SFs occurs along free edges, with lower SF concentrations in the interior of the cell. In summary, the results of this study suggest that cell spreading is driven by free energy minimization based on a competition between decreasing
The new view of hydrophobic free energy.
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.
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
Helmholtz bright and boundary solitons
Christian, J M [Joule Physics Laboratory, School of Computing, Science and Engineering, Institute for Materials Research, University of Salford, Salford M5 4WT (United Kingdom); McDonald, G S [Joule Physics Laboratory, School of Computing, Science and Engineering, Institute for Materials Research, University of Salford, Salford M5 4WT (United Kingdom); Chamorro-Posada, P [Departmento de TeorIa de la Senal y Comunicaciones e IngenierIa Telematica, Universidad de Valladolid, ETSI Telecomunicacion, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)
2007-02-16
We report, for the first time, exact analytical boundary solitons of a generalized cubic-quintic nonlinear Helmholtz (NLH) equation. These solutions have a linked-plateau topology that is distinct from conventional dark soliton solutions; their amplitude and intensity distributions are spatially delocalized and connect regions of finite and zero wave-field disturbances (suggesting also the classification as 'edge solitons'). Extensive numerical simulations compare the stability properties of recently derived Helmholtz bright solitons, for this type of polynomial nonlinearity, to those of the new boundary solitons. The latter are found to possess a remarkable stability characteristic, exhibiting robustness against perturbations that would otherwise lead to the destabilizing of their bright-soliton counterparts.
Helmholtz bright and boundary solitons
Christian, J M; McDonald, G S; Chamorro-Posada, P
2007-01-01
We report, for the first time, exact analytical boundary solitons of a generalized cubic-quintic nonlinear Helmholtz (NLH) equation. These solutions have a linked-plateau topology that is distinct from conventional dark soliton solutions; their amplitude and intensity distributions are spatially delocalized and connect regions of finite and zero wave-field disturbances (suggesting also the classification as 'edge solitons'). Extensive numerical simulations compare the stability properties of recently derived Helmholtz bright solitons, for this type of polynomial nonlinearity, to those of the new boundary solitons. The latter are found to possess a remarkable stability characteristic, exhibiting robustness against perturbations that would otherwise lead to the destabilizing of their bright-soliton counterparts
The free energy principle, negative energy modes, and stability
Morrison, P.J.; Kotschenreuther, M.
1990-01-01
This paper is concerned with instability of equilibria of Hamiltonian, fluid and plasma dynamical systems. Usually the dynamical equilibrium of interest is not the state of thermodynamic equilibrium, and does not correspond to a free energy minimum. The relaxation of this type of equilibrium is conventionally considered to be initiated by linear instability. However, there are many cases where linear instability is not present, but the equilibrium is nonlinearly unstable to arbitrarily small perturbations. This paper is about general free energy expressions for determining the presence of linear or nonlinear instabilities. These expressions are simple and practical, and can be obtained for all equilibria of all ideal fluid and plasma models. By free energy, we mean the energy change upon perturbations of the equilibrium that respect dynamical phase space constraints. This quantity is measured by a self-adjoint quadratic form, called δ 2 F. The free energy can result in instability when δ 2 F is indefinite; i.e. there exist accessible perturbations that lower the free energy of the system. A primary purpose of this paper is to tie together three manifestations of what we will refer to as negative energy modes. The first is the conventional plasma physics notion of negative energy mode that is based on the definition of the energy in a homogeneous dielectric medium. A negative energy mode is a normal mode of the medium (plasma) that possesses negative dielectric energy. The second manifestation occurs in finite degree-of-freedom Hamiltonian normal form theory. The quadratic part of a Hamiltonian in the vicinity of an equilibrium point, which possesses only distinct oscillatory eigenvalues, has an invariant signature. Thus in cases where the quadratic form is indefinite, it is natural to refer to the modes corresponding to the negative signature as negative energy modes
The Bogoliubov free energy functional II
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...
Calculating Free Energies Using Average Force
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.
Analysis of the Bogoliubov free energy functional
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...
Applications for Energy Recovering Free Electron Lasers
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.
An efficient Helmholtz solver for acoustic transversely isotropic media
Wu, Zedong
2017-11-11
The acoustic approximation, even for anisotropic media, is widely used in current industry imaging and inversion algorithms mainly because P-waves constitute the majority of the energy recorded in seismic exploration. The resulting acoustic formulas tend to be simpler, resulting in more efficient implementations, and depend on less medium parameters. However, conventional solutions of the acoustic wave equation with higher-order derivatives suffer from S-wave artifacts. Thus, we propose to separate the quasi-P wave propagation in anisotropic media into the elliptic anisotropic operator (free of the artifacts) and the non-elliptic-anisotropic components, which form a pseudo-differential operator. We, then, develop a separable approximation of the dispersion relation of non-elliptic-anisotropic components, specifically for transversely isotropic (TI) media. Finally, we iteratively solve the simpler lower-order elliptical wave equation for a modified source function that includes the non-elliptical terms represented in the Fourier domain. A frequency domain Helmholtz formulation of the approach renders the iterative implementation efficient as the cost is dominated by the Lower-Upper (LU) decomposition of the impedance matrix for the simpler elliptical anisotropic model. Also, the resulting wavefield is free of S-wave artifacts and has balanced amplitude. Numerical examples show that the method is reasonably accurate and efficient.
An efficient Helmholtz solver for acoustic transversely isotropic media
Wu, Zedong; Alkhalifah, Tariq Ali
2017-01-01
The acoustic approximation, even for anisotropic media, is widely used in current industry imaging and inversion algorithms mainly because P-waves constitute the majority of the energy recorded in seismic exploration. The resulting acoustic formulas tend to be simpler, resulting in more efficient implementations, and depend on less medium parameters. However, conventional solutions of the acoustic wave equation with higher-order derivatives suffer from S-wave artifacts. Thus, we propose to separate the quasi-P wave propagation in anisotropic media into the elliptic anisotropic operator (free of the artifacts) and the non-elliptic-anisotropic components, which form a pseudo-differential operator. We, then, develop a separable approximation of the dispersion relation of non-elliptic-anisotropic components, specifically for transversely isotropic (TI) media. Finally, we iteratively solve the simpler lower-order elliptical wave equation for a modified source function that includes the non-elliptical terms represented in the Fourier domain. A frequency domain Helmholtz formulation of the approach renders the iterative implementation efficient as the cost is dominated by the Lower-Upper (LU) decomposition of the impedance matrix for the simpler elliptical anisotropic model. Also, the resulting wavefield is free of S-wave artifacts and has balanced amplitude. Numerical examples show that the method is reasonably accurate and efficient.
KELVIN-HELMHOLTZ INSTABILITY OF A CORONAL STREAMER
Feng, L.; Gan, W. Q. [Key Laboratory of Dark Matter and Space Astronomy, Purple Mountain Observatory, Chinese Academy of Sciences, 210008 Nanjing (China); Inhester, B., E-mail: lfeng@pmo.ac.cn [Max-Planck-Institut fuer Sonnensystemforschung, Max-Planck-Str.2, D-37191 Katlenburg-Lindau (Germany)
2013-09-10
Shear-flow-driven instability can play an important role in energy transfer processes in coronal plasma. We present for the first time the observation of a kink-like oscillation of a streamer that is probably caused by the streaming kink-mode Kelvin-Helmholtz instability (KHI). The wave-like behavior of the streamer was observed by the Large Angle and Spectrometric Coronagraph Experiment C2 and C3 on board the SOlar and Heliospheric Observatory. The observed wave had a period of about 70-80 minutes, and its wavelength increased from 2 R{sub Sun} to 3 R{sub Sun} in about 1.5 hr. The phase speeds of its crests and troughs decreased from 406 {+-} 20 to 356 {+-} 31 km s{sup -1} during the event. Within the same heliocentric range, the wave amplitude also appeared to increase with time. We attribute the phenomena to the MHD KHI, which occurs at a neutral sheet in a fluid wake. The free energy driving the instability is supplied by the sheared flow and sheared magnetic field across the streamer plane. The plasma properties of the local environment of the streamer were estimated from the phase speed and instability threshold criteria.
The Magnetic Free Energy in Active Regions
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.
Free energy of formation of lanthanum nickelate
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
Is the Free Vacuum Energy Infinite?
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
Holographic free energy and thermodynamic geometry
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
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
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.)
Arbitrage-free valuation of energy derivatives
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
Assessment of CO2 free energy options
Cavlina, N.; Raseta, D.; Matutinovic, I.
2014-01-01
One of the European Union climate and energy targets is to significantly reduce CO 2 emissions, at least 20% by 2020, compared to 1990. In the power industry, most popular solution is use of solar and wind power. Since their production varies significantly during the day, for the purpose of base-load production they can be paired with gas-fired power plant. Other possible CO 2 -free solution is nuclear power plant. This article compared predicted cost of energy production for newly built nuclear power plant and newly built combination of wind or solar and gas-fired power plant. Comparison was done using Levelized Unit of Energy Cost (LUEC). Calculations were performed using the Monte Carlo method. For input parameters that have biggest uncertainty (gas cost, CO 2 emission fee) those uncertainties were addressed not only through probability distribution around predicted value, but also through different scenarios. Power plants were compared based on their economic lifetime. (authors)
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
Exploration, Novelty, Surprise and Free Energy Minimisation
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.
Free energy of mixing of acetone and methanol: a computer simulation investigation.
Idrissi, Abdenacer; Polok, Kamil; Barj, Mohammed; Marekha, Bogdan; Kiselev, Mikhail; Jedlovszky, Pál
2013-12-19
The change of the Helmholtz free energy, internal energy, and entropy accompanying the mixing of acetone and methanol is calculated in the entire composition range by the method of thermodynamic integration using three different potential model combinations of the two compounds. In the first system, both molecules are described by the OPLS, and in the second system, both molecules are described by the original TraPPE force field, whereas in the third system a modified version of the TraPPE potential is used for acetone in combination with the original TraPPE model of methanol. The results reveal that, in contrast with the acetone-water system, all of these three model combinations are able to reproduce the full miscibility of acetone and methanol, although the thermodynamic driving force of this mixing is very small. It is also seen, in accordance with the finding of former structural analyses, that the mixing of the two components is driven by the entropy term corresponding to the ideal mixing, which is large enough to overcompensate the effect of the energy increase and entropy loss due to the interaction of the unlike components in the mixtures. Among the three model combinations, the use of the original TraPPE model of methanol and modified TraPPE model of acetone turns out to be clearly the best in this respect, as it is able to reproduce the experimental free energy, internal energy, and entropy of mixing values within 0.15 kJ/mol, 0.2 kJ/mol, and 1 J/(mol K), respectively, in the entire composition range. The success of this model combination originates from the fact that the use of the modified TraPPE model of acetone instead of the original one in these mixtures improves the reproduction of the entropy of mixing, while it retains the ability of the original model of excellently reproducing the internal energy of mixing.
The Limit of Free Magnetic Energy in Active Regions
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.
Generalized formulation of free energy and application to photosynthesis
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.
Free Magnetic Energy and Coronal Heating
Winebarger, Amy; Moore, Ron; Falconer, David
2012-01-01
Previous work has shown that the coronal X-ray luminosity of an active region increases roughly in direct proportion to the total photospheric flux of the active region's magnetic field (Fisher et al. 1998). It is also observed, however, that the coronal luminosity of active regions of nearly the same flux content can differ by an order of magnitude. In this presentation, we analyze 10 active regions with roughly the same total magnetic flux. We first determine several coronal properties, such as X-ray luminosity (calculated using Hinode XRT), peak temperature (calculated using Hinode EIS), and total Fe XVIII emission (calculated using SDO AIA). We present the dependence of these properties on a proxy of the free magnetic energy of the active region
Postselection-free energy-time entanglement
Strekalov, D.V.; Pittman, T.B.; Sergienko, A.V.; Shih, Y.H.; Kwiat, P.G.
1996-01-01
We report a two-photon interference experiment that realizes a postselection-free test of Bell close-quote s inequality based on energy-time entanglement. In contrast with all previous experiments of this type, the employed entangled states are obtained without the use of a beam splitter or a short coincidence window to open-quote open-quote throw away close-quote close-quote unwanted amplitudes. A (95.0±1.4)% interference fringe visibility is observed, implying a strong violation of the Bell inequality. The scheme is very compact and has demonstrated excellent stability, suggesting that it may be useful, for example, in practical quantum cryptography. copyright 1996 The American Physical Society
Towards a fossil free energy future. The next energy transition
Lazarus, M.; Greber, L.; Hall, J.; Bartels, C.; Bernow, S.; Hansen, E.; Raskin, P.; Von Hippel, D. (Stockholm Environment Institute, Boston, MA (United States))
1993-04-01
The report provides technical analysis and documentation as input to the Greenpeace project 'Towards a fossil free energy future'. It presents a main scenario and several variants for reducing greenhouse gas emissions, and the technical methods and assumptions used to develop them. The goal is to investigate the technical, economic and policy feasibility to phasing out fossil fuels over the next century as part of a strategy to avert unacceptably high levels or rates of global warming. 209 refs., 42 figs., 27 tabs.
Linden, H. R.; Singer, S. F.
2001-12-01
It is generally agreed that hydrogen is an ideal energy source, both for transportation and for the generation of electric power. Through the use of fuel cells, hydrogen becomes a high-efficiency carbon-free power source for electromotive transport; with the help of regenerative braking, cars should be able to reach triple the current mileage. Many have visualized a distributed electric supply network with decentralized generation based on fuel cells. Fuel cells can provide high generation efficiencies by overcoming the fundamental thermodynamic limitation imposed by the Carnot cycle. Further, by using the heat energy of the high-temperature fuel cell in co-generation, one can achieve total thermal efficiencies approaching 100 percent, as compared to present-day average power-plant efficiencies of around 35 percent. In addition to reducing CO2 emissions, distributed generation based on fuel cells also eliminates the tremendous release of waste heat into the environment, the need for cooling water, and related limitations on siting. Manufacture of hydrogen remains a key problem, but there are many technical solutions that come into play whenever the cost equations permit . One can visualize both central and local hydrogen production. Initially, reforming of abundant natural gas into mixtures of 80% H2 and 20% CO2 provides a relatively low-emission source of hydrogen. Conventional fossil-fuel plants and nuclear plants can become hydrogen factories using both high-temperature topping cycles and electrolysis of water. Hydro-electric plants can manufacture hydrogen by electrolysis. Later, photovoltaic and wind farms could be set up at favorable locations around the world as hydrogen factories. If perfected, photovoltaic hydrogen production through catalysis would use solar photons most efficiently . For both wind and PV, hydrogen production solves some crucial problems: intermittency of wind and of solar radiation, storage of energy, and use of locations that are not
Temperature dependence of grain boundary free energy and elastic constants
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.
A Free Energy Model for Hysteresis Ferroelectric Materials
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...
Extraordinary acoustic transmission mediated by Helmholtz resonators
Vijay Koju
2014-07-01
Full Text Available We demonstrate perfect transmission of sound through a rigid barrier embedded with Helmholtz resonators. The resonators are confined within a waveguide and they are oriented such that one neck protrudes onto each side of the barrier. Perfect sound transmission occurs even though the open area of the necks is less than 3% of the barrier area. Maximum transmission occurs at the resonant frequency of the Helmholtz resonator. Because the dimensions of the Helmholtz resonators are much smaller than the resonant wavelength, the transmission is independent of the direction of sound on the barrier and of the relative placement of the necks. Further, we show that the transmitted sound experiences a continuous phase transition of π radians as a function of frequency through resonance. In simulations of adjacent resonators with slightly offset resonance frequencies, the phase difference leads to destructive interference. By expanding the simulation to a linear array of tuned Helmholtz resonators we show that it is possible to create an acoustic lens. The ability of Helmholtz resonator arrays to manipulate the phase of a plane acoustic wave enables a new class of sonic beam-forming devices analogous to diffractive optics.
Free-Energy Calculations. A Mathematical Perspective
Pohorille, Andrzej
2015-01-01
conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.
Diabat Interpolation for Polymorph Free-Energy Differences.
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.
Helmholtz and the psychophysiology of time.
Debru, C
2001-09-01
After having measured the velocity of the nervous impulse in the 1850s, Helmholtz began doing research on the temporal dimensions of visual perception. Experiments dealing with the velocity of propagation in nerves (as well as with aspects of perception) were carried out occasionally for some fifteen years until their final publication in 1871. Although the temporal dimension of perception seems to have interested Helmholtz less than problems of geometry and space, his experiments on the time of perception were technically rather subtle and seminal, especially compared with experiments performed by his contemporaries, such as Sigmund Exner, William James, Rudolf Hermann Lotze, Ernst Mach, Wilhelm Volkmann, and Wilhelm Wundt. Helmholtz's conception of the temporal aspects of perception reflects the continuity that holds between psychophysiological research and the Kantian philosophical background.
Free-energy coarse-grained potential for C60
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
A Short Essay on the Uses of Free Energy
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…
Cosmological constant versus free energy for heterotic strings
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.)
Calculation of molecular free energies in classical potentials
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)
Free energy from molecular dynamics with multiple constraints
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
On Helmholtz Problem for Plane Periodical Structures
Akishin, P.G.; Vinitskij, S.I.
1994-01-01
The plane Helmholtz problem of the periodical disc structures with the phase shifts conditions of the solutions along the basis lattice vectors and the Dirichlet conditions on the basic boundaries is considered. The Green function satisfying the quasi periodical conditions on the lattice is constructed. The Helmholtz problem is reduced to the boundary integral equations for the simple layer potentials of this Green function. The methods of the discretization of the arising integral equations are proposed. The procedures of calculation of the matrix elements are discussed. The reality of the spectral parameter of the nonlinear continuous and discretized problems is shown. 8 refs., 2 figs
Alternative Energy: A Guide to Free Information for Educators.
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)…
Calculation of the surface free energy of fcc copper nanoparticles
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
Free energy profiles from single-molecule pulling experiments.
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.
Völker, Benjamin; Landis, Chad M; Kamlah, Marc
2012-01-01
Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435–51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435–51). Full sets of adjusted free energy coefficients for PbTiO 3 and tetragonal Pb(Zr,Ti)O 3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed. (paper)
Probing Free-Energy Surfaces with Differential Scanning Calorimetry
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.
Free Magnetic Energy in Solar Active Regions above the Minimum-Energy Relaxed State
Regnier, S.; Priest, E. R.
2008-01-01
To understand the physics of solar flares, including the local reorganization of the magnetic field and the acceleration of energetic particles, we have first to estimate the free magnetic energy available for such phenomena, which can be converted into kinetic and thermal energy. The free magnetic energy is the excess energy of a magnetic configuration compared to the minimum-energy state, which is a linear force-free field if the magnetic helicity of the configuration is conserved. We inves...
Guidelines for the analysis of free energy calculations.
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.
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.
The free-energy cost of interaction between DNA loops.
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.
Free energy evaluation in polymer translocation via Jarzynski equality
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
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.
Surface free energy for systems with integrable boundary conditions
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
Information-to-free-energy conversion: Utilizing thermal fluctuations.
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.
Regeneralized London free energy for high-Tc vortex lattices
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 .
Implicit ligand theory for relative binding free energies
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.
Turbulent kinetic energy equation and free mixing
Morel, T.; Torda, T. P.; Bradshaw, P.
1973-01-01
Calculation of free shear flows was carried out to investigate the usefulness of several concepts which were previously successfully applied to wall flows. The method belongs to the class of differential approaches. The turbulence is taken into account by the introduction of one additional partial differential equation, the transport equation for the turbulent shear stress. The structure of turbulence is modeled after Bradshaw et al. This model was used successfully in boundary layers and its applicability to other flows is demonstrated. The work reported differs substantially from that of an earlier attempt to use this approach for calculation of free flows. The most important difference is that the region around the center line is treated by invoking the interaction hypothesis (concerning the structure of turbulence in the regions separated by the velocity extrema). The compressibility effects on shear layer spreading at low and moderate Mach numbers were investigated. In the absence of detailed experiments in free flows, the evidence from boundary layers that at low Mach numbers the structure of turbulence is unaffected by the compressibility was relied on. The present model was tested over a range of self-preserving and developing flows including pressure gradients using identical empirical input. The dependence of the structure of turbulence on the spreading rate of the shear layer was established.
Surface free energy of alkali and transition metal nanoparticles
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
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.
Standard free energy of formation of iron iodide
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.
Free energy distribution function of a random Ising ferromagnet
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
The free-energy principle: a unified brain theory?
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 surfaces in the superconducting mixed state
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-market approach to energy proposed in new study
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
QM/MM free energy simulations: recent progress and challenges
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
Learning free energy landscapes using artificial neural networks.
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.
Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.
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.
Learning free energy landscapes using artificial neural networks
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.
Accelerated weight histogram method for exploring free energy landscapes
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.
Levy-free part in energy tax is not wanted
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
Using the fast fourier transform in binding free energy calculations.
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.
Measuring excess free energies of self-assembled membrane structures.
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.
The Helmholtz legacy in physiological acoustics
Hiebert, Erwin
2014-01-01
This book explores the interactions between science and music in the late nineteenth- and early twentieth century. It examines and evaluates the work of Hermann von Helmholtz, Max Planck, Shohe Tanaka, and Adriaan Fokker, leading physicists and physiologists who were committed to understanding crucial aesthetic components of the art of music, including the standardization of pitch and the implementation of various types of intonations. With a mixture of physics, physiology, and aesthetics, author Erwin Hiebert addresses throughout the book how just intonation came to intersect with the history of keyboard instruments and exert an influence on the development of Western music. He begins with the work of Hermann von Helmholtz, a leading nineteenth-century physicist and physiologist who not only made important contributions in vision, optics, electrodynamics and thermodynamics, but also helped advanced the field of music theory as well. The author traces the Helmholtzian trends of thought that become inherently ...
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations
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
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.
Low energy quasi free scattering on nuclear surface
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.
Energy buildup in sheared force-free magnetic fields
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.
Computation of Hemagglutinin Free Energy Difference by the Confinement Method
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
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.
Helmholtz and Goethe -- controversies at the birth of modern neuroscience.
Kesselring, Jürg
2013-01-01
Hermann von Helmholtz (1821-1894), a great German scientist and philosopher, made his mark during the exciting twilight period from the Enlightenment and Romanticism to the beginnings of modern neuroscience and offered new perspectives through his work. His early inclination was for physics, which he found more attractive than purely geometric and algebraic studies, but his father was not able to make it possible for him to study physics, and so he studied medicine in order to earn a living. His lecture before the Physical Society in Berlin on July 23, 1847, 'about the conservation of the force' marked an epochal turn, even though his intention had been to deliver 'merely, some critical investigations and arrangement of facts in favor of the physiologists' as well as good arguments for the refusal of the theory of 'vitality'. Even though these new concepts were at first dismissed as fantastic speculation by some of the authorities in physics and philosophy of the day, they were enthusiastically welcomed by younger students of philosophy and the older men soon had to allow themselves to be persuaded that the effectiveness of vitality, though great and beautiful, is actually always dependent on some source of energy. Helmholtz critically assessed Goethe as a physical scientist but he did not dispute his great importance as a poet. Copyright © 2012 S. Karger AG, Basel.
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
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.
Variational Approach to Enhanced Sampling and Free Energy Calculations
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.
Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems
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.
Virtual substitution scan via single-step free energy perturbation.
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.
Novel Hyperbolic Homoclinic Solutions of the Helmholtz-Duffing Oscillators
Yang-Yang Chen
2016-01-01
Full Text Available The exact and explicit homoclinic solution of the undamped Helmholtz-Duffing oscillator is derived by a presented hyperbolic function balance procedure. The homoclinic solution of the self-excited Helmholtz-Duffing oscillator can also be obtained by an extended hyperbolic perturbation method. The application of the present homoclinic solutions to the chaos prediction of the nonautonomous Helmholtz-Duffing oscillator is performed. Effectiveness and advantage of the present solutions are shown by comparisons.
A Short Essay on the Uses of Free Energy
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...
Free energy surfaces from nonequilibrium processes without work measurement
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.
Free energy functionals for polarization fluctuations: Pekar factor revisited.
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
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).
Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations
Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.
2002-01-01
Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...
Relationship between wave energy and free energy from pickup ions in the Comet Halley environment
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.
Nie, Chu; Geng, Jun; Marlow, William H.
2016-01-01
In order to improve the sampling of restricted microstates in our previous work [C. Nie, J. Geng, and W. H. Marlow, J. Chem. Phys. 127, 154505 (2007); 128, 234310 (2008)] and quantitatively predict thermal properties of supersaturated vapors, an extension is made to the Corti and Debenedetti subcell constraint algorithm [D. S. Corti and P. Debenedetti, Chem. Eng. Sci. 49, 2717 (1994)], which restricts the maximum allowed local density at any point in a simulation box. The maximum allowed local density at a point in a simulation box is defined by the maximum number of particles N m allowed to appear inside a sphere of radius R, with this point as the center of the sphere. Both N m and R serve as extra thermodynamic variables for maintaining a certain degree of spatial homogeneity in a supersaturated system. In a restricted canonical ensemble, at a given temperature and an overall density, series of local minima on the Helmholtz free energy surface F(N m , R) are found subject to different (N m , R) pairs. The true equilibrium metastable state is identified through the analysis of the formation free energies of Stillinger clusters of various sizes obtained from these restricted states. The simulation results of a supersaturated Lennard-Jones vapor at reduced temperature 0.7 including the vapor pressure isotherm, formation free energies of critical nuclei, and chemical potential differences are presented and analyzed. In addition, with slight modifications, the current algorithm can be applied to computing thermal properties of superheated liquids.
Free energy barriers to evaporation of water in hydrophobic confinement.
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.
Funnel metadynamics as accurate binding free-energy method
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
The Free Energy in the Derrida-Retaux Recursive Model
Hu, Yueyun; Shi, Zhan
2018-05-01
We are interested in a simple max-type recursive model studied by Derrida and Retaux (J Stat Phys 156:268-290, 2014) in the context of a physics problem, and find a wide range for the exponent in the free energy in the nearly supercritical regime.
Calculating zeros: Non-equilibrium free energy calculations
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
Molecular dynamics simulations and free energy profile of ...
aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.
Free neutron-proton analyzing power at medium energies
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.)
Possible Lead Free Nanocomposite Dielectrics for High Energy Storage Applications
Srinivas Kurpati
2017-03-01
Full Text Available There is an increasing demand to improve the energy density of dielectric capacitors for satisfying the next generation material systems. One effective approach is to embed high dielectric constant inclusions such as lead zirconia titanate in polymer matrix. However, with the increasing concerns on environmental safety and biocompatibility, the need to expel lead (Pb from modern electronics has been receiving more attention. Using high aspect ratio dielectric inclusions such as nanowires could lead to further enhancement of energy density. Therefore, the present brief review work focuses on the feasibility of development of a lead-free nanowire reinforced polymer matrix capacitor for energy storage application. It is expected that Lead-free sodium Niobate nanowires (NaNbO3 and Boron nitride will be a future candidate to be synthesized using simple hydrothermal method, followed by mixing them with polyvinylidene fluoride (PVDF/ divinyl tetramethyl disiloxanebis (benzocyclobutene matrix using a solution-casting method for Nanocomposites fabrication. The energy density of NaNbO3 and BN based composites are also be compared with that of lead-containing (PbTiO3/PVDF Nano composites to show the feasibility of replacing lead-containing materials from high-energy density dielectric capacitors. Further, this paper explores the feasibility of these materials for space applications because of high energy storage capacity, more flexibility and high operating temperatures. This paper is very much useful researchers who would like to work on polymer nanocomposites for high energy storage applications.
Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao
2009-01-01
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
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.
Free-Free Transitions in the Presence of Laser Fields at Very Low Incident Electron Energy
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.
A new energy transfer model for turbulent free shear flow
Liou, William W.-W.
1992-01-01
A new model for the energy transfer mechanism in the large-scale turbulent kinetic energy equation is proposed. An estimate of the characteristic length scale of the energy containing large structures is obtained from the wavelength associated with the structures predicted by a weakly nonlinear analysis for turbulent free shear flows. With the inclusion of the proposed energy transfer model, the weakly nonlinear wave models for the turbulent large-scale structures are self-contained and are likely to be independent flow geometries. The model is tested against a plane mixing layer. Reasonably good agreement is achieved. Finally, it is shown by using the Liapunov function method, the balance between the production and the drainage of the kinetic energy of the turbulent large-scale structures is asymptotically stable as their amplitude saturates. The saturation of the wave amplitude provides an alternative indicator for flow self-similarity.
Free Electron Laser as Energy Driver for Inertial Confinement Fusion
Saldin, E.L.; Shnejdmiller, E.A.; Ul'yanov, Yu.N.; Sarantsev, V.P.; Yurkov, M.V.
1994-01-01
A FEL based energy driver for Inertial Confinement Fusion (ICF) is proposed. The key element of the scheme is free electron laser system. Novel technical solutions reveal a possibility to construct the FEL system operating at radiation wavelength λ = 0.5 μm and providing flash energy E = 1 MJ and brightness 4 x 10 22 W cm -2 sr -1 within steering pulse duration 0.1-2 ns. Total energy efficiency of the proposed ICF energy driver is about of 11% and repetition rate is 40 Hz. Dimensions of such an ICF driver are comparable with those of heavy-ion ICF driver, while the problem of technical realization seems to be more realistic. It is shown that the FEL based ICF energy driver may be constructed at the present level of accelerator technique R and D. 27 refs., 10 figs., 3 tabs
Interfacial free energy and stiffness of aluminum during rapid solidification
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.
Free energy option and its relevance to improve domestic energy demands in southern Nigeria
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.
CFD simulation of Kelvin-Helmholtz instability
Strubelj, L.; Tiselj, I.
2005-01-01
Kelvin-Helmholtz instability appears in stratified two-fluid flow at surface. When the relative velocity is higher than the critical relative velocity, the growth of waves occurs. The experiment of Thorpe [1] used as a benchmark in the present paper, is made in a rectangular glass tube filled with two immiscible fluids of various densities. We simulated the growth of instability with CFX-5.7 code and compared simulation with analytical solution. It was found that surface tension force, which stabilizes growth of waves, actually has a destabilizing effect in simulation, unless very small timestep and residual is used. In CFX code system of nonlinear Navier-Stokes equations is linearised and solved iterative in each timestep, until prescribed residual is achieved. On the other hand, simulation without surface tension force is more stable than analytical result predicts. (author)
Characterizing permanent magnet blocks with Helmholtz coils
Carnegie, D. W.; Timpf, J.
1992-08-01
Most of the insertion devices to be installed at the Advanced Photon Source will utilize permanent magnets in their magnetic structures. The quality of the spectral output is sensitive to the errors in the field of the device which are related to variations in the magnetic properties of the individual blocks. The Advanced Photon Source will have a measurement facility to map the field in the completed insertion devices and equipment to test and modify the magnetic strength of the individual magnet blocks. One component of the facility, the Helmholtz coil permanent magnet block measurement system, has been assembled and tested. This system measures the total magnetic moment vector of a block with a precision better than 0.01% and a directional resolution of about 0.05°. The design and performance of the system will be presented.
Nonlocal Free Energy of a Spatially Inhomogeneous Superconductor
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)
Solid/liquid interfacial free energies in binary systems
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.
FESetup: Automating Setup for Alchemical Free Energy Simulations.
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.
Free energy landscape and molecular pathways of gas hydrate nucleation
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-01-01
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Free energy landscape and molecular pathways of gas hydrate nucleation.
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-12-07
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Surface free energy analysis of adsorbents used for radioiodine adsorption
González-García, C.M.; Román, S.; González, J.F.; Sabio, E.; Ledesma, B.
2013-01-01
In this work, the surface free energy of biomass-based activated carbons, both fresh and impregnated with triethylenediamine, has been evaluated. The contribution of Lifshitz van der Waals components was determined by the model proposed by van Oss et al. The results obtained allowed predicting the most probable configurations of the impregnant onto the carbon surface and its influence on the subsequent adsorption of radioactive methyl iodide.
Free energy landscape and molecular pathways of gas hydrate nucleation
Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)
2016-12-07
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy
Minh, David D. L.; Adib, Artur B.
2008-05-01
An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.
Characterizing structural transitions using localized free energy landscape analysis.
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.
Hydrogen role in a carbon-free energy mix
2014-02-01
Among the energy storage technologies under development today, there is today an increasing interest towards the hydrogen-based ones. Hydrogen generation allows to store electricity, while its combustion can supply electrical, mechanical or heat energy. The French Atomic Energy Commission (CEA) started to work on hydrogen technologies at the end of the 1990's in order to reinforce its economical interest. The development of these technologies is one of the 34 French industrial programs presented in September 2013 by the French Minister of productive recovery. This paper aims at identifying the hydrogen stakes in a carbon-free energy mix and at highlighting the remaining technological challenges to be met before reaching an industrial development level
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.
Energy and the NAFTA [North American Free Trade Agreement
Plourde, A.
1993-01-01
A review is presented of the implications of the North American Free Trade Agreement (NAFTA) for the energy industry. This agreement expands the coverage accorded to energy in the Canada-US Free Trade Agreement (FTA), and is of limited significance with respect to Canada-US relations, but is quite important to these two countries' energy trade with Mexico. With respect to Canada-US trade, the most important departure from the FTA is that NAFTA tends to ensure a greater degree of respect for the terms of negotiated contracts, in particular by requiring the parties to make efforts to secure compliance with the national treatment provisions of the NAFTA by subfederal regulatory entities. Mexico's constitution severely restricts foreign participation in the activities of its energy industries, including basic petrochemicals. While NAFTA accomodates these restrictions, Canadian and US companies will have opportunities to bid on contracts for goods and services and construction in the Mexican energy sector on an equal footing with their Mexican counterparts. NAFTA also provides expanded opportunities for foreign investment and control in electricity generation for own-use, cogeneration and public service purposes. The parties are explicitly allowed to extend activity incentives to their respective oil and gas industries. 9 refs
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
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
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
Determination of partial molar volumes from free energy perturbation theory.
Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L
2015-04-07
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.
Determination of partial molar volumes from free energy perturbation theory†
Vilseck, Jonah Z.; Tirado-Rives, Julian
2016-01-01
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343
Mass and free energy of Lovelock black holes
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.
Emotional valence and the free-energy principle.
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.
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.
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)...
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.
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.
Exploring the free energy surfaces of clusters using reconnaissance metadynamics
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.
Variationally Optimized Free-Energy Flooding for Rate Calculation
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.
Approximate scaling properties of RNA free energy landscapes
Baskaran, S.; Stadler, P. F.; Schuster, P.
1996-01-01
RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.
Bifurcation-free design method of pulse energy converter controllers
Kolokolov, Yury; Ustinov, Pavel; Essounbouli, Najib; Hamzaoui, Abdelaziz
2009-01-01
In this paper, a design method of pulse energy converter (PEC) controllers is proposed. This method develops a classical frequency domain design, based on the small signal modeling, by means of an addition of a nonlinear dynamics analysis stage. The main idea of the proposed method consists in fact that the PEC controller, designed with an application of the small signal modeling, is tuned after with taking into the consideration an essentially nonlinear nature of the PEC that makes it possible to avoid bifurcation phenomena in the PEC dynamics at the design stage (bifurcation-free design). Also application of the proposed method allows an improvement of the designed controller performance. The application of this bifurcation-free design method is demonstrated on an example of the controller design of direct current-direct current (DC-DC) buck converter with an input electromagnetic interference filter.
Free-energy landscape of a hyperstable RNA tetraloop.
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.
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
McCarty, J; Clark, A J; Copperman, J; Guenza, M G
2014-05-28
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.
Trp-cage: Folding free energy landscape in explicit water
Zhou, Ruhong
2003-11-01
Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.
Minimal Self-Models and the Free Energy Principle
Jakub eLimanowski
2013-09-01
Full Text Available The term "minimal phenomenal selfhood" describes the basic, pre-reflective experience of being a self (Blanke & Metzinger, 2009. Theoretical accounts of the minimal self have long recognized the importance and the ambivalence of the body as both part of the physical world, and the enabling condition for being in this world (Gallagher, 2005; Grafton, 2009. A recent account of minimal phenomenal selfhood (MPS, Metzinger, 2004a centers on the consideration that minimal selfhood emerges as the result of basic self-modeling mechanisms, thereby being founded on pre-reflective bodily processes. The free energy principle (FEP, Friston, 2010 is a novel unified theory of cortical function that builds upon the imperative that self-organizing systems entail hierarchical generative models of the causes of their sensory input, which are optimized by minimizing free energy as an approximation of the log-likelihood of the model. The implementation of the FEP via predictive coding mechanisms and in particular the active inference principle emphasizes the role of embodiment for predictive self-modeling, which has been appreciated in recent publications. In this review, we provide an overview of these conceptions and illustrate thereby the potential power of the FEP in explaining the mechanisms underlying minimal selfhood and its key constituents, multisensory integration, interoception, agency, perspective, and the experience of mineness. We conclude that the conceptualization of MPS can be well mapped onto a hierarchical generative model furnished by the free energy principle and may constitute the basis for higher-level, cognitive forms of self-referral, as well as the understanding of other minds.
MHD Kelvin-Helmholtz instability in non-hydrostatic equilibrium
Laghouati, Y; Bouabdallah, A; Zizi, M; Alemany, A
2007-01-01
The present work deals with the linear stability of a magnetohydrodynamic shear flow so that a stratified inviscid fluid rotating about a vertical axis when a uniform magnetic field is applied in the direction of the streaming or zonal flow. In geophysical flow, the stability of the flow is determined by taking into account the nonhydrostatic condition depending on Richardson number R i and the deviation δ from hydrostatic equilibrium. According to Stone (Stone P H 1971 J. Fluid. Mech. 45 659), it is shown that such deviation δ decreases the growth rates of three kinds of instability which can appear as geostrophic (G), symmetric (S) and Kelvin-Helmholtz (K-H) instabilities. To be specific, the evolution of the flow is therefore considered in the light of the influence of magnetic field, particularly, on K-H instability. The results of this study are presented by the linear stability of a magnetohydrodynamic, with horizontal free-shear flow of stratified fluid, subject to rotation about the vertical axis and uniform magnetic field in the zonal direction. Results are discussed and compared to previous works as Chandrasekhar (Chandrasekhar S 1961 Hydrodynamic and hydromagnetic stability (Oxford: Clarendon Press) chapter 11 pp 481-513) and Stone
Wettability and surface free energy of polarised ceramic biomaterials
Nakamura, Miho; Hori, Naoko; Namba, Saki; Yamashita, Kimihiro; Toyama, Takeshi; Nishimiya, Nobuyuki
2015-01-01
The surface modification of ceramic biomaterials used for medical devices is expected to improve osteoconductivity through control of the interfaces between the materials and living tissues. Polarisation treatment induced surface charges on hydroxyapatite, β-tricalcium phosphate, carbonate-substituted hydroxyapatite and yttria-stabilized zirconia regardless of the differences in the carrier ions participating in the polarisation. Characterization of the surfaces revealed that the wettability of the polarised ceramic biomaterials was improved through the increase in the surface free energies compared with conventional ceramic surfaces. (note)
Trivial constraints on orbital-free kinetic energy density functionals
Luo, Kai; Trickey, S. B.
2018-03-01
Approximate kinetic energy density functionals (KEDFs) are central to orbital-free density functional theory. Limitations on the spatial derivative dependencies of KEDFs have been claimed from differential virial theorems. We identify a central defect in the argument: the relationships are not true for an arbitrary density but hold only for the minimizing density and corresponding chemical potential. Contrary to the claims therefore, the relationships are not constraints and provide no independent information about the spatial derivative dependencies of approximate KEDFs. A simple argument also shows that validity for arbitrary v-representable densities is not restored by appeal to the density-potential bijection.
Advancing Drug Discovery through Enhanced Free Energy Calculations.
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
Free electron lasers for transmission of energy in space
Segall, S. B.; Hiddleston, H. R.; Catella, G. C.
1981-01-01
A one-dimensional resonant-particle model of a free electron laser (FEL) is used to calculate laser gain and conversion efficiency of electron energy to photon energy. The optical beam profile for a resonant optical cavity is included in the model as an axial variation of laser intensity. The electron beam profile is matched to the optical beam profile and modeled as an axial variation of current density. Effective energy spread due to beam emittance is included. Accelerators appropriate for a space-based FEL oscillator are reviewed. Constraints on the concentric optical resonator and on systems required for space operation are described. An example is given of a space-based FEL that would produce 1.7 MW of average output power at 0.5 micrometer wavelength with over 50% conversion efficiency of electrical energy to laser energy. It would utilize a 10 m-long amplifier centered in a 200 m-long optical cavity. A 3-amp, 65 meV electrostatic accelerator would provide the electron beam and recover the beam after it passes through the amplifier. Three to five shuttle flights would be needed to place the laser in orbit.
Iterative solution of the Helmholtz equation
Larsson, E.; Otto, K. [Uppsala Univ. (Sweden)
1996-12-31
We have shown that the numerical solution of the two-dimensional Helmholtz equation can be obtained in a very efficient way by using a preconditioned iterative method. We discretize the equation with second-order accurate finite difference operators and take special care to obtain non-reflecting boundary conditions. We solve the large, sparse system of equations that arises with the preconditioned restarted GMRES iteration. The preconditioner is of {open_quotes}fast Poisson type{close_quotes}, and is derived as a direct solver for a modified PDE problem.The arithmetic complexity for the preconditioner is O(n log{sub 2} n), where n is the number of grid points. As a test problem we use the propagation of sound waves in water in a duct with curved bottom. Numerical experiments show that the preconditioned iterative method is very efficient for this type of problem. The convergence rate does not decrease dramatically when the frequency increases. Compared to banded Gaussian elimination, which is a standard solution method for this type of problems, the iterative method shows significant gain in both storage requirement and arithmetic complexity. Furthermore, the relative gain increases when the frequency increases.
The Helmholtz Hierarchy: Phase Space Statistics of Cold Dark Matter
Tassev, Svetlin
2010-01-01
We present a new formalism to study large-scale structure in the universe. The result is a hierarchy (which we call the "Helmholtz Hierarchy") of equations describing the phase space statistics of cold dark matter (CDM). The hierarchy features a physical ordering parameter which interpolates between the Zel'dovich approximation and fully-fledged gravitational interactions. The results incorporate the effects of stream crossing. We show that the Helmholtz hierarchy is self-consistent and obeys...
Simulation of Helmholtz Resonance Effects in Aircraft ECS
Pollok, Alexander; Schröffer, Andreas
2017-01-01
Helmholtz resonators are closed volumes that are connected to pipes. They exhibit a pronounced resonance frequency, where small boundary pressure excitations in the volume or the environment lead to large mass flow excitations in the pipe. Aircraft have a topology similar to Helmholtz resonators, the closed volume is represented by the cabin, while the pipe is represented by the Environmental Control System. Some discrepancies appear due to the non-zero mass-flow or friction effects in...
Kelvin-Helmholtz evolution in subsonic cold streams feeding galaxies
Angulo, Adrianna; Coffing, S.; Kuranz, C.; Drake, R. P.; Klein, S.; Trantham, M.; Malamud, G.
2017-10-01
The most prolific star formers in cosmological history lie in a regime where dense filament structures carried substantial mass into the galaxy to sustain star formation without producing a shock. However, hydrodynamic instabilities present on the filament surface limit the ability of such structures to deliver dense matter deeply enough to sustain star formation. Simulations lack the finite resolution necessary to allow fair treatment of the instabilities present at the stream boundary. Using the Omega EP laser, we simulate this mode of galaxy formation with a cold, dense, filament structure within a hotter, subsonic flow and observe the interface evolution. Machined surface perturbations stimulate the development of the Kelvin-Helmholtz (KH) instability due to the resultant shear between the two media. A spherical crystal imaging system produces high-resolution radiographs of the KH structures along the filament surface. The results from the first experiments of this kind, using a rod with single-mode, long-wavelength modulations, will be discussed. This work is funded by the U.S. Department of Energy, through the NNSA-DS and SC-OFES Joint Program in High-Energy-Density Laboratory Plasmas, Grant Number DE-NA0002956, and the National Laser User Facility Program, Grant Number DE-NA0002719, and through.
Coarse-grained versus atomistic simulations : realistic interaction free energies for real proteins
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
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
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
Low-energy electron inelastic mean free path in materials
Nguyen-Truong, Hieu T., E-mail: nguyentruongthanhhieu@tdt.edu.vn [Theoretical Physics Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 756636 (Viet Nam)
2016-04-25
We show that the dielectric approach can determine electron inelastic mean free paths in materials with an accuracy equivalent to those from first-principle calculations in the GW approximation of many-body theory. The present approach is an alternative for calculating the hot-electron lifetime, which is an important quantity in ultrafast electron dynamics. This approach, applied here to solid copper for electron energies below 100 eV, yields results in agreement with experimental data from time-resolved two-photon photoemission, angle-resolved photoelectron spectroscopy, and X-ray absorption fine structure measurements in the energy ranges 2–3.5, 10–15, and 60–100 eV, respectively.
New theory of radiative energy transfer in free electromagnetic fields
Wolf, E.
1976-01-01
A new theory of radiative energy transfer in free, statistically stationary electromagnetic fields is presented. It provides a model for energy transport that is rigorous both within the framework of the stochastic theory of the classical field as well as within the framework of the theory of the quantized field. Unlike the usual phenomenological model of radiative energy transfer that centers around a single scalar quantity (the specific intensity of radiation), our theory brings into evidence the need for characterizing the energy transport by means of two (related) quantities: a scalar and a vector that may be identified, in a well-defined sense, with ''angular components'' of the average electromagnetic energy density and of the average Poynting vector, respectively. Both of them are defined in terms of invariants of certain new electromagnetic correlation tensors. In the special case when the field is statistically homogeneous, our model reduces to the usual one and our angular component of the average electromagnetic energy density, when multiplied by the vacuum speed of light, then acquires all the properties of the specific intensity of radiation. When the field is not statistically homogeneous our model approximates to the usual phenomenological one, provided that the angular correlations between plane wave modes of the field extend over a sufficiently small solid angle of directions about the direction of propagation of each mode. It is tentatively suggested that, when suitably normalized, our angular component of the average electromagnetic energy density may be interpreted as a quasi-probability (general quantum-mechancial phase-space distribution function, such as Wigner's) for the position and the momentum of a photon
Experimental realization of extraordinary acoustic transmission using Helmholtz resonators
Brian C. Crow
2015-02-01
Full Text Available The phenomenon of extraordinary acoustic transmission through a solid barrier with an embedded Helmholtz resonator (HR is demonstrated. The Helmholtz resonator consists of an embedded cavity and two necks that protrude, one on each side of the barrier. Extraordinary transmission occurs for a narrow spectral range encompassing the resonant frequency of the Helmholtz resonator. We show that an amplitude transmission of 97.5% is achieved through a resonator whose neck creates an open area of 6.25% of the total barrier area. In addition to the enhanced transmission, we show that there is a smooth, continuous phase transition in the transmitted sound as a function of frequency. The frequency dependent phase transition is used to experimentally realize slow wave propagation for a narrow-band Gaussian wave packet centered at the maximum transmission frequency. The use of parallel pairs of Helmholtz resonators tuned to different resonant frequencies is experimentally explored as a means of increasing the transmission bandwidth. These experiments show that because of the phase transition, there is always a frequency between the two Helmholtz resonant frequencies at which destructive interference occurs whether the resonances are close or far apart. Finally, we explain how the phase transition associated with Helmholtz-resonator-mediated extraordinary acoustic transmission can be exploited to produce diffractive acoustic components including sub-wavelength thickness acoustic lenses.
Non-Equilibrium Properties from Equilibrium Free Energy Calculations
Pohorille, Andrew; Wilson, Michael A.
2012-01-01
Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.
Diffusion in multicomponent systems: a free energy approach
Emmanuel, Simon; Cortis, Andrea; Berkowitz, Brian
2004-01-01
This work examines diffusion in ternary non-ideal systems and derives coupled non-linear equations based on a non-equilibrium thermodynamic approach in which an explicit expression for the free energy is substituted into standard diffusion equations. For ideal solutions, the equations employ four mobility parameters (M aa , M ab , M ba , and M bb ), and uphill diffusion is predicted for certain initial conditions and combinations of mobilities. For the more complex case of ternary Simple Mixtures, two non-ideality parameters (χ ac and χ bc ) that are directly related to the excess free energy of mixing are introduced. The solution of the equations is carried out by means of two different numerical schemes: (1) spectral collocation and (2) finite element. An error minimization technique is coupled with the spectral collocation method and applied to diffusional profiles to extract the M and χ parameters. The model satisfactorily reproduces diffusional profiles from published data for silicate melts. Further improvements in numerical and experimental techniques are then suggested
Free energy landscape of a minimalist salt bridge model.
Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei
2016-01-01
Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.
Flavour fields in steady state: stress tensor and free energy
Banerjee, Avik; Kundu, Arnab; Kundu, Sandipan
2016-01-01
The dynamics of a probe brane in a given gravitational background is governed by the Dirac-Born-Infeld action. The corresponding open string metric arises naturally in studying the fluctuations on the probe. In Gauge-String duality, it is known that in the presence of a constant electric field on the worldvolume of the probe, the open string metric acquires an event horizon and therefore the fluctuation modes on the probe experience an effective temperature. In this article, we bring together various properties of such a system to a formal definition and a subsequent narration of the effective thermodynamics and the stress tensor of the corresponding flavour fields, also including a non-vanishing chemical potential. In doing so, we point out a potentially infinitely-degenerate scheme-dependence of regularizing the free energy, which nevertheless yields a universal contribution in certain cases. This universal piece appears as the coefficient of a log-divergence in free energy when a space-filling probe brane is embedded in AdS d+1 -background, for d=2,4, and is related to conformal anomaly. For the special case of d=2, the universal factor has a striking resemblance to the well-known heat current formula in (1+1)-dimensional conformal field theory in steady-state, which endows a plausible physical interpretation to it. Interestingly, we observe a vanishing conformal anomaly in d=6.
Inference with minimal Gibbs free energy in information field theory
Ensslin, Torsten A.; Weig, Cornelius
2010-01-01
Non-linear and non-Gaussian signal inference problems are difficult to tackle. Renormalization techniques permit us to construct good estimators for the posterior signal mean within information field theory (IFT), but the approximations and assumptions made are not very obvious. Here we introduce the simple concept of minimal Gibbs free energy to IFT, and show that previous renormalization results emerge naturally. They can be understood as being the Gaussian approximation to the full posterior probability, which has maximal cross information with it. We derive optimized estimators for three applications, to illustrate the usage of the framework: (i) reconstruction of a log-normal signal from Poissonian data with background counts and point spread function, as it is needed for gamma ray astronomy and for cosmography using photometric galaxy redshifts, (ii) inference of a Gaussian signal with unknown spectrum, and (iii) inference of a Poissonian log-normal signal with unknown spectrum, the combination of (i) and (ii). Finally we explain how Gaussian knowledge states constructed by the minimal Gibbs free energy principle at different temperatures can be combined into a more accurate surrogate of the non-Gaussian posterior.
Iterative free-energy optimization for recurrent neural networks (INFERNO)
2017-01-01
The intra-parietal lobe coupled with the Basal Ganglia forms a working memory that demonstrates strong planning capabilities for generating robust yet flexible neuronal sequences. Neurocomputational models however, often fails to control long range neural synchrony in recurrent spiking networks due to spontaneous activity. As a novel framework based on the free-energy principle, we propose to see the problem of spikes’ synchrony as an optimization problem of the neurons sub-threshold activity for the generation of long neuronal chains. Using a stochastic gradient descent, a reinforcement signal (presumably dopaminergic) evaluates the quality of one input vector to move the recurrent neural network to a desired activity; depending on the error made, this input vector is strengthened to hill-climb the gradient or elicited to search for another solution. This vector can be learned then by one associative memory as a model of the basal-ganglia to control the recurrent neural network. Experiments on habit learning and on sequence retrieving demonstrate the capabilities of the dual system to generate very long and precise spatio-temporal sequences, above two hundred iterations. Its features are applied then to the sequential planning of arm movements. In line with neurobiological theories, we discuss its relevance for modeling the cortico-basal working memory to initiate flexible goal-directed neuronal chains of causation and its relation to novel architectures such as Deep Networks, Neural Turing Machines and the Free-Energy Principle. PMID:28282439
Energy Pooling Upconversion in Free Space and Optical Cavities
LaCount, Michael D.
energy pooling rate efficiency of 99%. This demonstrates that the energy pooling rate can be made faster than its competing processes. Based on the results of this study, a set of design rules was developed to optimize the rate efficiency of energy pooling. Prior to this research, no attempt had been made to determine if energy pooling could be made to out-pace competing processes--i.e. whether or not a molecular system could be designed to utilize energy pooling as an efficient means of upconversion. This initial investigation was part of a larger effort involving a team of researchers at the University of Colorado, Boulder and at the National Renewable Energy Laboratory. After establishing our computational proof-of-concept, we collectively used the new design rules to select an improved system for energy pooling. This consisted of rhodamine 6G and stilbene-420. These molecules were fabricated into a thin film, and the maximum internal quantum yield was measured to be 36% under sufficiently high intensity light. To further increase the efficiency of energy pooling, encapsulation within optical cavities was considered as a way of changing the rate of processes characterized by electric dipole-dipole coupling. This was carried out using a combination of classical electromagnetism, quantum electrodynamics, and perturbation theory. It was found that, in the near field, if the distance of the energy transfer is smaller than the distance from the energy transfer site and the cavity wall, then the electric dipole-dipole coupling tensor is not influenced by the cavity environment and the rates of energy transfer processes are the same as those in free space. Any increase in energy transfer efficiencies that are experimentally measured must therefore be caused by changing the rate of light absorption and emission. This is an important finding because earlier, less rigorous studies had concluded otherwise. It has been previously demonstrated that an optical cavity can be used to
Examining ion channel properties using free-energy methods.
Domene, Carmen; Furini, Simone
2009-01-01
Recent advances in structural biology have revealed the architecture of a number of transmembrane channels, allowing for these complex biological systems to be understood in atomistic detail. Computational simulations are a powerful tool by which the dynamic and energetic properties, and thereby the function of these protein architectures, can be investigated. The experimentally observable properties of a system are often determined more by energetic than dynamics, and therefore understanding the underlying free energy (FE) of biophysical processes is of crucial importance. Critical to the accurate evaluation of FE values are the problems of obtaining accurate sampling of complex biological energy landscapes, and of obtaining accurate representations of the potential energy of a system, this latter problem having been addressed through the development of molecular force fields. While these challenges are common to all FE methods, depending on the system under study, and the questions being asked of it, one technique for FE calculation may be preferable to another, the choice of method and simulation protocol being crucial to achieve efficiency. Applied in a correct manner, FE calculations represent a predictive and affordable computational tool with which to make relevant contact with experiments. This chapter, therefore, aims to give an overview of the most widely implemented computational methods used to calculate the FE associated with particular biochemical or biophysical events, and to highlight their recent applications to ion channels. Copyright © 2009 Elsevier Inc. All rights reserved.
Environmental protection through energy conservation: A free lunch at last?
Ruff, L.E.
1990-01-01
A cautious analysis of demand-side management programs is presented. Utility demand-side management (DSM) programs deserve to be given full and careful consideration as a potential way to give consumers better end-use energy services for their money, utilities an edge in an increasingly competitive market, and society a way to reduce the environmental costs of energy production. But in each of these areas, DSM programs offer no free lunches and have no inherent advantages over supply-side programs. If energy conservation makes sense on economic and business grounds, it can meet the standard economic and business tests applied to most of the rest of the economy; it neither requires nor deserves to be exempt from market concepts and disciplines. If utility DSM programs make sense on environmental grounds, they should be able to demonstrate their cost-effectiveness relative to other, primarily supply-side measures society is willing to undertake in order to control environmental effects. Subsidizing DSM measures in the hope that something good will happen far upstream can waste much money and cause disappointment and frustration
Thermodynamic free-energy minimization for unsupervised fusion of dual-color infrared breast images
Szu, Harold; Miao, Lidan; Qi, Hairong
2006-04-01
function [A] may vary from the point tumor to its neighborhood, we could not rely on neighborhood statistics as did in a popular unsupervised independent component analysis (ICA) mathematical statistical method, we instead impose the physics equilibrium condition of the minimum of Helmholtz free-energy, H = E - T °S. In case of the point breast cancer, we can assume the constant ground state energy E ° to be normalized by those benign neighborhood tissue, and then the excited state can be computed by means of Taylor series expansion in terms of the pixel I/O data. We can augment the X-ray mammogram technique with passive IR imaging to reduce the unwanted X-rays during the chemotherapy recovery. When the sequence is animated into a movie, and the recovery dynamics is played backward in time, the movie simulates the cameras' potential for early detection without suffering the PD=0.1 search uncertainty. In summary, we applied two satellite-grade dual-color IR imaging cameras and advanced military (automatic target recognition) ATR spectrum fusion algorithm at the middle wavelength IR (3 - 5μm) and long wavelength IR (8 - 12μm), which are capable to screen malignant tumors proved by the time-reverse fashion of the animated movie experiments. On the contrary, the traditional thermal breast scanning/imaging, known as thermograms over decades, was IR spectrum-blind, and limited to a single night-vision camera and the necessary waiting for the cool down period for taking a second look for change detection suffers too many environmental and personnel variabilities.
Gibbs free energy of formation of UPb(s) compound
Samui, Pradeep; Agarwal, Renu; Mishra, Ratikanta
2012-01-01
Liquid lead and lead-bismuth eutectic (LBE) are being explored as primary candidates for coolants in accelerator driven systems and in advanced nuclear reactors due to their favorable thermo-physical and chemical properties. They are also proposed to be used as spallation neutron source in ADS Reactor Systems. However, corrosion of structural materials (i.e. steel) presents a critical challenge for the use of liquid lead or LBE in advanced nuclear reactors. The interactions of liquid lead or LBE with clad and fuel is of great scientific and technological importance in the development of advanced nuclear reactors. Clad failure/breach can lead to reaction of coolant elements with fuel components. Thus the study of fuel-coolant interaction of U with Pb/Bi is important. The paper deals with the determination of Gibbs free energy of formation of U-rich phase i.e. UPb in Pb-U system, employing Knudsen effusion mass loss technique
Ising model on tangled chain - 1: Free energy and entropy
Mejdani, R.
1993-04-01
In this paper we have considered an Ising model defined on tangled chain, in which more bonds have been added to those of pure Ising chain. to understand their competition, particularly between ferromagnetic and antiferromagnetic bonds, we have studied, using the transfer matrix method, some simple analytical calculations and an iterative algorithm, the behaviour of the free energy and entropy, particularly in the zero-field and zero temperature limit, for different configurations of the ferromagnetic tangled chain and different types of addition interaction (ferromagnetic or antiferromagnetic). We found that the condition J=J' between the ferromagnetic interaction J along the chain and the antiferromagnetic interaction J' across the chain is somewhat as a ''transition-region'' condition for this behaviour. Our results indicate also the existence of non-zero entropy at zero temperature. (author). 17 refs, 8 figs
The puckering free-energy surface of proline
Di Wu
2013-03-01
Full Text Available Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χj (j = 1∼5 as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ2 pathway (χ2 is about the Cβ—Cγ bond is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods.
The Emissions-Free Energy (EFE) Working Group
Humphries, R., E-mail: Roger.Humphries@amec.com [AMEC NSS, Toronto, Ontario (Canada)
2014-07-01
There has been a growing international interest in smaller, simpler reactors for generating electricity and process heat. They incorporate modern technological advances in reactor design, reactor safety, modular construction, proliferation resistance, and risk reduction. The interest in these reactors has been driven by many factors, including the need to reduce greenhouse gas emissions and provide reliable power in 'off-grid' or 'edge-of-grid' locations. Licensing these new small reactors, particularly in Canada's resource rich remote northern regions, will raises issues in a wide variety of technical, institutional, socio-economic and regulatory policy areas. The first small reactor vendor to file a license application or to engage the CNSC in its pre-licensing vendor design review process is going to have to deal with these issues. However these issues affect the entire small reactor industry and it is essential that the industry as a whole address them. Accordingly, a small reactor industry-wide Working Group has been established to identify and prioritize the issues that need to be addressed and work with the CNSC and other interested stakeholders to agree on a resolution acceptable to all parties. The objective of the small reactor industry is to introduce an economical, emissions-free source of electrical and thermal energy. It is the opinion of the WG that our emphasis ought to be on the product rather than the technology, hence the name Emissions-Free Energy Working Group. The EFE WG has initiated contact with the CNSC and has started its review of CNSC draft regulatory and guidance documents. (author)
Exploration, Sampling, And Reconstruction of Free Energy Surfaces with Gaussian Process Regression.
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.
The regulated energy economy versus the free energy market - The West German experience
Liesen, K.; Schwarz, H.O.
1989-09-01
The overall good performance of the West German energy industry in terms of energy policy objectives such as security of supplies, competitiveness, efficient use of energy and environmental protection, is attributable to an energy policy based on the principles of the market economy and steady application of these same principles. Today, though, a debate, at times controversial, on whether more market influence or more government intervention is required is underway in West Germany; in view of the successes of energy policy and the balance struck between free enterprise and the government in the past, this debate has met with little understanding in some quarters. It is generally agreed, though, that the quality of the challenges energy policy and the energy industry in West Germany will confront in the future will remain essentially unchanged. West German energy policy will have to deal with: reestablishing a consensus on coal and nuclear power policy; achieving a high standard of environmental protection in the European Communities, and strengthening the position of the energy industry as efforts are made to get moves underway to create a single European market for energy underway. No fundamental change in the course of energy policy in the Federal Republic of Germany is needed to solve current energy policy issues or to preserve the underlying goals of this policy. An energy policy which continues to give priority where possible to market mechanisms as a means of adjustment and provides energy suppliers and users with a stable and reliable framework in which to operate, offers the best promise for meeting the challenges of the future. (author). 2 figs
Finite-size corrections to the free energies of crystalline solids
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
Xiang, Zhexin; Soto, Cinque S; Honig, Barry
2002-05-28
In this paper, we introduce a method to account for the shape of the potential energy curve in the evaluation of conformational free energies. The method is based on a procedure that generates a set of conformations, each with its own force-field energy, but adds a term to this energy that favors conformations that are close in structure (have a low rmsd) to other conformations. The sum of the force-field energy and rmsd-dependent term is defined here as the "colony energy" of a given conformation, because each conformation that is generated is viewed as representing a colony of points. The use of the colony energy tends to select conformations that are located in broad energy basins. The approach is applied to the ab initio prediction of the conformations of all of the loops in a dataset of 135 nonredundant proteins. By using an rmsd from a native criterion based on the superposition of loop stems, the average rmsd of 5-, 6-, 7-, and 8-residue long loops is 0.85, 0.92, 1.23, and 1.45 A, respectively. For 8-residue loops, 60 of 61 predictions have an rmsd of less than 3.0 A. The use of the colony energy is found to improve significantly the results obtained from the potential function alone. (The loop prediction program, "Loopy," can be downloaded at http://trantor.bioc.columbia.edu.)
Bistable dark solitons of a cubic-quintic Helmholtz equation
Christian, J. M.; McDonald, G. S.; Chamorro-Posada, P.
2010-01-01
We provide a report on exact analytical bistable dark spatial solitons of a nonlinear Helmholtz equation with a cubic-quintic refractive-index model. Our analysis begins with an investigation of the modulational instability characteristics of Helmholtz plane waves. We then derive a dark soliton by mapping the desired asymptotic form onto a uniform background field and obtain a more general solution by deploying rotational invariance laws in the laboratory frame. The geometry of the new soliton is explored in detail, and a range of new physical predictions is uncovered. Particular attention is paid to the unified phenomena of arbitrary-angle off-axis propagation and nondegenerate bistability. Crucially, the corresponding solution of paraxial theory emerges in a simultaneous multiple limit. We conclude with a set of computer simulations that examine the role of Helmholtz dark solitons as robust attractors.
On the TAP Free Energy in the Mixed p-Spin Models
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.
Heavy-quark free energies, internal-energy and entropy contributions
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.)
The Helmholtz Hierarchy: phase space statistics of cold dark matter
Tassev, Svetlin V.
2011-01-01
We present a new formalism to study large-scale structure in the universe. The result is a hierarchy (which we call the ''Helmholtz Hierarchy'') of equations describing the phase space statistics of cold dark matter (CDM). The hierarchy features a physical ordering parameter which interpolates between the Zel'dovich approximation and fully-fledged gravitational interactions. The results incorporate the effects of stream crossing. We show that the Helmholtz hierarchy is self-consistent and obeys causality to all orders. We present an interpretation of the hierarchy in terms of effective particle trajectories
Helmholtz solitons in power-law optical materials
Christian, J. M.; McDonald, G. S.; Potton, R. J.; Chamorro-Posada, P.
2007-01-01
A nonlinear Helmholtz equation for optical materials with regimes of power-law type of nonlinearity is proposed. This model captures the evolution of broad beams at any angle with respect to the reference direction in a wide range of media, including some semiconductors, doped glasses, and liquid crystals. Exact analytical soliton solutions are presented for a generic nonlinearity, within which known Kerr solitons comprise a subset. Three general conservation laws are also reported. Analysis and numerical simulations examine the stability of the Helmholtz power-law solitons. A propagation feature, associated with spatial solitons in power-law media, constituting a class of oscillatory solution, is identified
Bistable Helmholtz solitons in cubic-quintic materials
Christian, J. M.; McDonald, G. S.; Chamorro-Posada, P.
2007-01-01
We propose a nonlinear Helmholtz equation for modeling the evolution of broad optical beams in media with a cubic-quintic intensity-dependent refractive index. This type of nonlinearity is appropriate for some semiconductor materials, glasses, and polymers. Exact analytical soliton solutions are presented that describe self-trapped nonparaxial beams propagating at any angle with respect to the reference direction. These spatially symmetric solutions are, to the best of our knowledge, the first bistable Helmholtz solitons to be derived. Accompanying conservation laws (both integral and particular forms) are also reported. Numerical simulations investigate the stability of the solitons, which appear to be remarkably robust against perturbations
Mey, Antonia S. J. S.; Jiménez, Jordi Juárez; Michel, Julien
2018-01-01
The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.
Chemical Disequilibria and Sources of Gibbs Free Energy Inside Enceladus
Zolotov, M. Y.
2010-12-01
Non-photosynthetic organisms use chemical disequilibria in the environment to gain metabolic energy from enzyme catalyzed oxidation-reduction (redox) reactions. The presence of carbon dioxide, ammonia, formaldehyde, methanol, methane and other hydrocarbons in the eruptive plume of Enceladus [1] implies diverse redox disequilibria in the interior. In the history of the moon, redox disequilibria could have been activated through melting of a volatile-rich ice and following water-rock-organic interactions. Previous and/or present aqueous processes are consistent with the detection of NaCl and Na2CO3/NaHCO3-bearing grains emitted from Enceladus [2]. A low K/Na ratio in the grains [2] and a low upper limit for N2 in the plume [3] indicate low temperature (possibly enzymes if organisms were (are) present. The redox conditions in aqueous systems and amounts of available Gibbs free energy should have been affected by the production, consumption and escape of hydrogen. Aqueous oxidation of minerals (Fe-Ni metal, Fe-Ni phosphides, etc.) accreted on Enceladus should have led to H2 production, which is consistent with H2 detection in the plume [1]. Numerical evaluations based on concentrations of plume gases [1] reveal sufficient energy sources available to support metabolically diverse life at a wide range of activities (a) of dissolved H2 (log aH2 from 0 to -10). Formaldehyde, carbon dioxide [c.f. 4], HCN (if it is present), methanol, acetylene and other hydrocarbons have the potential to react with H2 to form methane. Aqueous hydrogenations of acetylene, HCN and formaldehyde to produce methanol are energetically favorable as well. Both favorable hydrogenation and hydration of HCN lead to formation of ammonia. Condensed organic species could also participate in redox reactions. Methane and ammonia are the final products of these putative redox transformations. Sulfates may have not formed in cold and/or short-term aqueous environments with a limited H2 escape. In contrast to
The global mean energy balance under cloud-free conditions
Wild, Martin; Hakuba, Maria; Folini, Dois; Ott, Patricia; Long, Charles
2017-04-01
A long standing problem of climate models is their overestimation of surface solar radiation not only under all-sky, but also under clear-sky conditions (Wild et al. 1995, Wild et al. 2006). This overestimation reduced over time in consecutive model generations due to the simulation of stronger atmospheric absorption. Here we analyze the clear sky fluxes of the latest climate model generation from the Coupled Model Intercomparison Project Phase 5 (CMIP5) against an expanded and updated set of direct observations from the Baseline Surface Radiation Network (BSRN). Clear sky climatologies from these sites have been composed based on the Long and Ackermann (2000) clear sky detection algorithm (Hakuba et al. 2017), and sampling issues when comparing with model simulated clear sky fluxes have been analyzed in Ott (2017). Overall, the overestimation of clear sky insolation in the CMIP5 models is now merely 1-2 Wm-2 in the multimodel mean, compared to 4 Wm-2 in CMIP3 and 6 Wm-2 in AMIPII (Wild et al. 2006). Still a considerable spread in the individual model biases is apparent, ranging from -2 Wm-2 to 10 Wm-2 when averaged over 53 globally distributed BSRN sites. This bias structure is used to infer best estimates for present day global mean clear sky insolation, following an approach developped in Wild et al. (2013, 2015, Clim. Dyn.) for all sky fluxes. Thereby the flux biases in the various models are linearly related to their respective global means. A best estimate can then be inferred from the linear regression at the intersect where the bias against the surface observations becomes zero. This way we obtain a best estimate of 247 Wm-2 for the global mean insolation at the Earth surface under cloud free conditions, and a global mean absorbed solar radiation of 214 Wm-2 in the cloud-free atmosphere, assuming a global mean surface albedo of 13.5%. Combined with a best estimate for the net influx of solar radiation at the Top of Atmosphere under cloud free conditions
From quantum chemical formation free energies to evaporation rates
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.
Multivariable extrapolation of grand canonical free energy landscapes
Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.
2017-12-01
We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.
Free-energy minimization and the dark-room problem.
Friston, Karl; Thornton, Christopher; Clark, Andy
2012-01-01
Recent years have seen the emergence of an important new fundamental theory of brain function. This theory brings information-theoretic, Bayesian, neuroscientific, and machine learning approaches into a single framework whose overarching principle is the minimization of surprise (or, equivalently, the maximization of expectation). The most comprehensive such treatment is the "free-energy minimization" formulation due to Karl Friston (see e.g., Friston and Stephan, 2007; Friston, 2010a,b - see also Fiorillo, 2010; Thornton, 2010). A recurrent puzzle raised by critics of these models is that biological systems do not seem to avoid surprises. We do not simply seek a dark, unchanging chamber, and stay there. This is the "Dark-Room Problem." Here, we describe the problem and further unpack the issues to which it speaks. Using the same format as the prolog of Eddington's Space, Time, and Gravitation (Eddington, 1920) we present our discussion as a conversation between: an information theorist (Thornton), a physicist (Friston), and a philosopher (Clark).
Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.
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.
Direct measurement of the free energy of aging hard sphere colloidal glasses.
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.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
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
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.
Reply to Comment on 'On the importance of the free energy for elasticity under pressure'
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)
An implicit finite-difference operator for the Helmholtz equation
Chu, Chunlei; Stoffa, Paul L.
2012-01-01
We have developed an implicit finite-difference operator for the Laplacian and applied it to solving the Helmholtz equation for computing the seismic responses in the frequency domain. This implicit operator can greatly improve the accuracy of the simulation results without adding significant extra computational cost, compared with the corresponding conventional explicit finite-difference scheme. We achieved this by taking advantage of the inherently implicit nature of the Helmholtz equation and merging together the two linear systems: one from the implicit finite-difference discretization of the Laplacian and the other from the discretization of the Helmholtz equation itself. The end result of this simple yet important merging manipulation is a single linear system, similar to the one resulting from the conventional explicit finite-difference discretizations, without involving any differentiation matrix inversions. We analyzed grid dispersions of the discrete Helmholtz equation to show the accuracy of this implicit finite-difference operator and used two numerical examples to demonstrate its efficiency. Our method can be extended to solve other frequency domain wave simulation problems straightforwardly. © 2012 Society of Exploration Geophysicists.
Reconstruction of extended sources for the Helmholtz equation
Kress, Rainer; Rundell, William
2013-01-01
The basis of most imaging methods is to detect hidden obstacles or inclusions within a body when one can only make measurements on an exterior surface. Our underlying model is that of inverse acoustic scattering based on the Helmholtz equation. Our
An implicit finite-difference operator for the Helmholtz equation
Chu, Chunlei
2012-07-01
We have developed an implicit finite-difference operator for the Laplacian and applied it to solving the Helmholtz equation for computing the seismic responses in the frequency domain. This implicit operator can greatly improve the accuracy of the simulation results without adding significant extra computational cost, compared with the corresponding conventional explicit finite-difference scheme. We achieved this by taking advantage of the inherently implicit nature of the Helmholtz equation and merging together the two linear systems: one from the implicit finite-difference discretization of the Laplacian and the other from the discretization of the Helmholtz equation itself. The end result of this simple yet important merging manipulation is a single linear system, similar to the one resulting from the conventional explicit finite-difference discretizations, without involving any differentiation matrix inversions. We analyzed grid dispersions of the discrete Helmholtz equation to show the accuracy of this implicit finite-difference operator and used two numerical examples to demonstrate its efficiency. Our method can be extended to solve other frequency domain wave simulation problems straightforwardly. © 2012 Society of Exploration Geophysicists.
Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.
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
The free energy landscape of small molecule unbinding.
Danzhi Huang
2011-02-01
Full Text Available The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide and eleven (5-diethylamino-2-pentanone non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics of ligand unbinding.
The calculation of surface free energy based on embedded atom method for solid nickel
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.
Heavy quark free energies for three quark systems at finite temperature
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.
Craddock, David
2008-01-01
Studies have shown that the average North American family will spend more than a quarter of a million dollars on energy in a lifetime. What many other countries, including Germany, Spain, France, Denmark, China, Brazil, and even Iceland, have realized is that there is a better way to power our homes, businesses, and cars by using renewable energy sources. Recently, the United States has begun to understand the importance of reducing its reliance on coal, natural gas, nuclear power, and hydropower plants, which comprise the majority of the nation's electricity, due to increasing oil prices.
Free energy change of off-eutectic binary alloys on solidification
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.
A simple free energy for the isotropic-nematic phase transition of rods
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
Constructing a multidimensional free energy surface like a spider weaving a web.
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.
Free energy on a cycle graph and trigonometric deformation of heat kernel traces on odd spheres
Kan, Nahomi; Shiraishi, Kiyoshi
2018-01-01
We consider a possible ‘deformation’ of the trace of the heat kernel on odd dimensional spheres, motivated by the calculation of the free energy of a scalar field on a discretized circle. By using an expansion in terms of the modified Bessel functions, we obtain the values of the free energies after a suitable regularization.
Designed azurins show lower reorganization free energies for intraprotein electron transfer
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...
Incorporating the effect of ionic strength in free energy calculations using explicit ions
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
CAN THE STABILITY OF PROTEIN MUTANTS BE PREDICTED BY FREE-ENERGY CALCULATIONS
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
Direct evaluation of free energy for large system through structure integration approach.
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.
Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.
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
Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.
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.
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.
Smart Energy Choices Free Up Dollars for Capital Improvements.
Ritchey, David
2003-01-01
Describes several ways to design or renovate school building to save thousand of dollars of energy costs. Considers site design, energy-efficient building envelope, renewable energy systems, lighting and electrical systems, mechanical and ventilation systems, water conservation, and transportation. Describes how to obtain information about the…
Towards a Continental Energy Market: From the Energy Crisis to the Free Trade Agreement, 1970-88.
Bennett, Paul W.
1989-01-01
Discusses the impact the 1973 oil embargo and resulting energy crisis had on Canadian energy policies, which eventually led in 1987 to the enactment of the Free Trade Agreement between Canada and the United States. Includes excerpts of three documents which reveal much about the shift in Canadian policy toward a continental energy market. (LS)
Bhatia, Anand
2012-01-01
We study the free-free transition in electron-helium ion in the ground state and embedded in a Debye potential in the presence of an external laser field at very low incident electron energies. The laser field is treated classically while the collision dynamics is treated quantum mechanically. The laser field is chosen as monochromatic, linearly polarized and homogeneous. The incident electron is considered to be dressed by the laser field in a nonperturbative manner by choosing Volkov wave function for it. The scattering wave function for the incident electron on the target embedded in a Debye potential is solved numerically by taking into account the effect of electron exchange. We calculate the laser-assisted differential and total cross sections for free-free transition for absorption/emission of a single photon or no photon exchange. The results will be presented at the conference.
Inquiries into the Nature of Free Energy and Entropy in Respect to Biochemical Thermodynamics
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 TDSÃ‚Â° of the Gibbs standard free energy relation DGÃ‚Â°= DHÃ‚Â°-TDSÃ‚Â° serves to account for differences or changes in nonthermal energies that do not contribute to DGÃ‚Â° and that, since DHÃ‚Â° serves to account for differences or changes in total energy, complete enthalpy-entropy (DHÃ‚Â° - TDSÃ‚Â° compensation must invariably occur in isothermal processes for which TDSÃ‚Â° 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
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.)
Acoustic superlens using Helmholtz-resonator-based metamaterials
Yang, Xishan; Yin, Jing; Yu, Gaokun; Peng, Linhui; Wang, Ning
2015-01-01
Acoustic superlens provides a way to overcome the diffraction limit with respect to the wavelength of the bulk wave in air. However, the operating frequency range of subwavelength imaging is quite narrow. Here, an acoustic superlens is designed using Helmholtz-resonator-based metamaterials to broaden the bandwidth of super-resolution. An experiment is carried out to verify subwavelength imaging of double slits, the imaging of which can be well resolved in the frequency range from 570 to 650 Hz. Different from previous works based on the Fabry-Pérot resonance, the corresponding mechanism of subwavelength imaging is the Fano resonance, and the strong coupling between the neighbouring Helmholtz resonators separated at the subwavelength interval leads to the enhanced sound transmission over a relatively wide frequency range
Fourier-Based Fast Multipole Method for the Helmholtz Equation
Cecka, Cris
2013-01-01
The fast multipole method (FMM) has had great success in reducing the computational complexity of solving the boundary integral form of the Helmholtz equation. We present a formulation of the Helmholtz FMM that uses Fourier basis functions rather than spherical harmonics. By modifying the transfer function in the precomputation stage of the FMM, time-critical stages of the algorithm are accelerated by causing the interpolation operators to become straightforward applications of fast Fourier transforms, retaining the diagonality of the transfer function, and providing a simplified error analysis. Using Fourier analysis, constructive algorithms are derived to a priori determine an integration quadrature for a given error tolerance. Sharp error bounds are derived and verified numerically. Various optimizations are considered to reduce the number of quadrature points and reduce the cost of computing the transfer function. © 2013 Society for Industrial and Applied Mathematics.
Voluntarism in early psychology: the case of Hermann von Helmholtz.
De Kock, Liesbet
2014-05-01
The failure to recognize the programmatic similarity between (post-)Kantian German philosophy and early psychology has impoverished psychology's historical self-understanding to a great extent. This article aims to contribute to recent efforts to overcome the gaps in the historiography of contemporary psychology, which are the result of an empiricist bias. To this end, we present an analysis of the way in which Hermann von Helmholtz's theory of perception resonates with Johann Gottlieb Fichte's Ego-doctrine. It will be argued that this indebtedness is particularly clear when focusing on the foundation of the differential awareness of subject and object in perception. In doing so, the widespread reception of Helmholtz's work as proto-positivist or strictly empiricist is challenged, in favor of the claim that important elements of his theorizing can only be understood properly against the background of Fichte's Ego-doctrine. PsycINFO Database Record (c) 2014 APA, all rights reserved.
Calculation of the beam injector steering system using Helmholtz coils
Passaro, A.; Sircilli Neto, F.; Migliano, A.C.C.
1991-03-01
In this work, a preliminary evaluation of the beam injector steering system of the IEAv electron linac is presented. From the existing injector configuration and with the assumptions of monoenergetic beam (100 keV) and uniform magnetic field, two pairs of Helmholtz coils were calculated for the steering system. Excitations of 105 A.turn and 37 A.turn were determined for the first and second coils, respectively. (author)
Thin-Layer Solutions of the Helmholtz and Related Equations
Ockendon, J. R.
2012-01-01
This paper concerns a certain class of two-dimensional solutions to four generic partial differential equations-the Helmholtz, modified Helmholtz, and convection-diffusion equations, and the heat conduction equation in the frequency domain-and the connections between these equations for this particular class of solutions.S pecifically, we consider thin-layer solutions, valid in narrow regions across which there is rapid variation, in the singularly perturbed limit as the coefficient of the Laplacian tends to zero.F or the wellstudied Helmholtz equation, this is the high-frequency limit and the solutions in question underpin the conventional ray theory/WKB approach in that they provide descriptions valid in some of the regions where these classical techniques fail.E xamples are caustics, shadow boundaries, whispering gallery, and creeping waves and focusing and bouncing ball modes.It transpires that virtually all such thin-layer models reduce to a class of generalized parabolic wave equations, of which the heat conduction equation is a special case. Moreover, in most situations, we will find that the appropriate parabolic wave equation solutions can be derived as limits of exact solutions of the Helmholtz equation.W e also show how reasonably well-understood thin-layer phenomena associated with any one of the four generic equations may translate into less well-known effects associated with the others.In addition, our considerations also shed some light on the relationship between the methods of matched asymptotic, WKB, and multiple-scales expansions. © 2012 Society for Industrial and Applied Mathematics.
Kelvin-Helmholtz instability in a weakly ionized layer
Shadmehri, Mohsen; Downes, Turlough P.
2007-01-01
We study the linear theory of Kelvin-Helmholtz instability in a layer of ions and neutrals with finite thickness. In the short wavelength limit the thickness of the layer has a negligible effect on the growing modes. However, perturbations with wavelength comparable to layer's thickness are significantly affected by the thickness of the layer. We show that the thickness of the layer has a stabilizing effect on the two dominant growing modes. Transition between the modes not only depends on th...
High Energy, Lead-Free Ignition Formulation for Thermate
Tracy, Gene
2002-01-01
... in the AN-Ml4 thermate grenade. This lead-free formulation has provided reliable ignition of the XM89 over a temperature range of -25 degrees F - 120 degrees F when using the M201 Al fuze as the initiator...
Is free knowledge transfer history in the energy sector?
Zewald, H.
2000-01-01
The European power industry is gradually changing from a government-controlled sector of monopolists to an internationally privatized free sector. Companies that used to cooperate are now competing with one another. The question is: can the international knowledge transfer institutes escape from this competitive climate or will they fall victim to it?
Energy dissipation of free exciton polaritons in semiconducting films
De Crescenzi, M.; Harbeke, G.; Tosatti, E.
1978-08-01
The effective (thickness-dependent) light absorption coefficient K(ω,d) is discussed for thin semiconducting films in the frequency range of free, spatially dispersive exciton polaritons. We find that (i) it oscillates strongly for small film thicknesses; (ii) it exhibits a slanted peak lineshape; (iii) its integrated strength also depends upon the exciton damping and extrapolates to zero for vanishing damping
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
Computational Approach to Explore the B/A Junction Free Energy in DNA.
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 analysis of spin models on hyperbolic lattice geometries.
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.
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.
The elastic free energy of a tandem modular protein under force.
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.
Calculation of free-energy differences from computer simulations of initial and final states
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
Nuclear energy in a nuclear weapon free world
Pilat, Joseph [Los Alamos National Laboratory
2009-01-01
The prospect of a nuclear renaissance has revived a decades old debate over the proliferation and terrorism risks of the use of nuclear power. This debate in the last few years has taken on an added dimension with renewed attention to disarmament. Increasingly, concerns that proliferation risks may reduce the prospects for realizing the vision of a nuclear-weapon-free world are being voiced.
Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.
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.
Inequalities for magnetic-flux free energies and confinement in lattice gauge theories
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.)
Gibbs free energy of formation of liquid lanthanide-bismuth alloys
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
Magnetic energy dissipation in force-free jets
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.
ENERGY BUDGETS IN FREE-LIVING GREEN IGUANAS IN A SEASONAL ENVIRONMENT
LICHTENBELT, WDV; WESSELINGH, RA; VOGEL, JT; ALBERS, KBM
Using a variety of techniques we estimated energy expenditure and allocation of energy in free-living green iguanas (Iguana iguana) in a seasonal environment on Curacao, Netherlands Antilles. 1) Daily energy expenditure (DEE) was measured by means of the doubly labeled water (DLW) technique, using
Effects of Energy Chirp on Echo-Enabled Harmonic Generation Free-Electron Lasers
Huang, Z.
2009-01-01
We study effects of energy chirp on echo-enabled harmonic generation (EEHG). Analytical expressions are compared with numerical simulations for both harmonic and bunching factors. We also discuss the EEHG free-electron laser bandwidth increase due to an energy-modulated beam and its pulse length dependence on the electron energy chirp
Naumov, Sergej; von Sonntag, Clemens
2011-11-01
Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.
Sheng, Qin, E-mail: Qin_Sheng@baylor.edu [Department of Mathematics and Center for Astrophysics, Space Physics and Engineering Research, Baylor University, One Bear Place, Waco, TX 76798-7328 (United States); Sun, Hai-wei, E-mail: hsun@umac.mo [Department of Mathematics, University of Macau (Macao)
2016-11-15
This study concerns the asymptotic stability of an eikonal, or ray, transformation based Peaceman–Rachford splitting method for solving the paraxial Helmholtz equation with high wave numbers. Arbitrary nonuniform grids are considered in transverse and beam propagation directions. The differential equation targeted has been used for modeling propagations of high intensity laser pulses over a long distance without diffractions. Self-focusing of high intensity beams may be balanced with the de-focusing effect of created ionized plasma channel in the situation, and applications of grid adaptations are frequently essential. It is shown rigorously that the fully discretized oscillation-free decomposition method on arbitrary adaptive grids is asymptotically stable with a stability index one. Simulation experiments are carried out to illustrate our concern and conclusions.
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
Binding free energy analysis of protein-protein docking model structures by evERdock.
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.
High-energy inverse free-electron laser accelerator
Courant, E.D.; Pellegrini, C.; Zakowicz, W.
1985-01-01
We study the inverse free electron laser (IFEL) accelerator and show that it can accelerate electrons to the few hundred GeV region with average acceleration rates of the order of 200 meV/m. Several possible accelerating structures are analyzed, and the effect of synchrotron radiation losses is studied. The longitudinal phase stability of accelerated particles is also analyzed. A Hamiltonian description, which takes into account the dissipative features of the IFEL accelerator, is introduced to study perturbations from the resonant acceleration. Adiabatic invariants are obtained and used to estimate the change of the electron phase space density during the acceleration process
The free energies of partially open coronal magnetic fields
Low, B. C.; Smith, D. F.
1993-01-01
A simple model of the low corona is examined in terms of a static polytropic atmosphere in equilibrium with a global magnetic field. The question posed is whether magnetostatic states with partially open magnetic fields may contain magnetic energies in excess of those in fully open magnetic fields. Based on the analysis presented here, it is concluded that the cross-field electric currents in the pre-eruption corona are a viable source of the bulk of the energies in a mass ejection and its associated flare.
The free energy of Maxwell-Vlasov equilibria
Morrison, P.J.; Pfirsch, D.
1989-10-01
A previously derived expression for the energy of arbitrary perturbations about arbitrary Vlasov-Maxwell equilibria is transformed into a very compact form. The new form is also obtained by a canonical transformation method for solving Vlasov's equation, which is based on Lie group theory. This method is simpler than the one used before and provides better physical insight. Finally a procedure is presented for determining the existence of negative-energy modes. In this context the question of why there is an accessibility constraint for the particles, but not for the fields, is discussed. 16 refs
Yavari, M., E-mail: yavari@iaukashan.ac.ir [Islamic Azad University, Kashan Branch (Iran, Islamic Republic of)
2016-06-15
We generalize the results of Nesterenko [13, 14] and Gogilidze and Surovtsev [15] for DNA structures. Using the generalized Hamiltonian formalism, we investigate solutions of the equilibrium shape equations for the linear free energy model.
Knot soliton in DNA and geometric structure of its free-energy density.
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.
Olson, Mark
2004-01-01
... screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase...
Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.
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.
The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.
Xu, You; Villa, Alessandra; Nilsson, Lennart
2017-06-05
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Free energy change of a dislocation due to a Cottrell atmosphere
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 fast tomographic method for searching the minimum free energy path
Chen, Changjun; Huang, Yanzhao; Xiao, Yi; Jiang, Xuewei
2014-01-01
Minimum Free Energy Path (MFEP) provides a lot of important information about the chemical reactions, like the free energy barrier, the location of the transition state, and the relative stability between reactant and product. With MFEP, one can study the mechanisms of the reaction in an efficient way. Due to a large number of degrees of freedom, searching the MFEP is a very time-consuming process. Here, we present a fast tomographic method to perform the search. Our approach first calculates the free energy surfaces in a sequence of hyperplanes perpendicular to a transition path. Based on an objective function and the free energy gradient, the transition path is optimized in the collective variable space iteratively. Applications of the present method to model systems show that our method is practical. It can be an alternative approach for finding the state-to-state MFEP
Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations
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.
An asymptotic formula for the free energy density of ideal quantum gases
Mackowiak, J.
1988-01-01
It is shown that the expressions for the free energy density of ideal quantum gases in the canonical and grand canonical ensembles, are identical up to additive terms which vanish in the thermodynamic limit. (orig.)
A free energy study of the liquid-liquid phase transition of the Jagla ...
Appendix” preliminary free energy surface calculations for select parameterizations of the generalized family of Jagla potentials spanning from the original (anomalous,water-like) Jagla model to the Lennard-Jones model. These calculations ...
Kuehn, T. J.; Nawrocki, P. M.
1978-01-01
It is suggested that federal programs for hastening the adoption of alternative energy sources must operate within the free market structure. Five phases of the free market commercialization process are described. Federal role possibilities include information dissemination and funding to stimulate private sector activities within these five phases, and federally sponsored procedures for accelerating commercialization of solar thermal small power systems are considered.
A Low-Energy-Spread Rf Accelerator for a Far-Infrared Free-Electron Laser
van der Geer, C. A. J.; Bakker, R. J.; van der Meer, A. F. G.; van Amersfoort, P. W.; Gillespie, W. A.; Saxon, G.; Poole, M. W.
1993-01-01
A high electron current and a small energy spread are essential for the operation of a free electron laser (FEL). In this paper we discuss the design and performance of the accelerator for FELIX, the free electron laser for infrared experiments. The system consists of a thermionic gun, a prebuncher,
Wai, C. M.; Hutchinson, S. G.
1989-01-01
Discusses the calculation of free energy in reactions between silicon dioxide and carbon. Describes several computer programs for calculating the free energy minimization and their uses in chemistry classrooms. Lists 16 references. (YP)
Designing lead-free antiferroelectrics for energy storage
Xu, Bin; Íñiguez, Jorge; Bellaiche, L.
2017-01-01
Dielectric capacitors, although presenting faster charging/discharging rates and better stability compared with supercapacitors or batteries, are limited in applications due to their low energy density. Antiferroelectric (AFE) compounds, however, show great promise due to their atypical polarization-versus-electric field curves. Here we report our first-principles-based theoretical predictions that Bi1−xRxFeO3 systems (R being a lanthanide, Nd in this work) can potentially allow high energy densities (100–150 J cm−3) and efficiencies (80–88%) for electric fields that may be within the range of feasibility upon experimental advances (2–3 MV cm−1). In addition, a simple model is derived to describe the energy density and efficiency of a general AFE material, providing a framework to assess the effect on the storage properties of variations in doping, electric field magnitude and direction, epitaxial strain, temperature and so on, which can facilitate future search of AFE materials for energy storage. PMID:28555655
Free energy diagram for the heterogeneous enzymatic hydrolysis of glycosidic bonds in cellulose
Westh, Peter; Cruys-Bagger, Nicolaj; Sørensen, Trine Holst
2015-01-01
for all stable and activated complexes defined by the reaction scheme, and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association...... no influence on the transition state for association, but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association....
A Python tool to set up relative free energy calculations in GROMACS.
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.
Roy, Arijit; Gururajan, M P
2017-01-01
A wide variety of morphologies arise due to the tetragonal anisotropy in interfacial free energy. In this paper, we report on a family of Extended Cahn-Hilliard (ECH) models for incorporating tetragonal anisotropy in interfacial free energy. We list the non-zero and independent parameters that are introduced in our model and list the constraints on them. For appropriate choice of these parameters, our model can produce a many of the morphologies seen in tetragonal systems such as di-pyramids,...
SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.
Petukh, Marharyta; Dai, Luogeng; Alexov, Emil
2016-04-12
Predicting the effect of amino acid substitutions on protein-protein affinity (typically evaluated via the change of protein binding free energy) is important for both understanding the disease-causing mechanism of missense mutations and guiding protein engineering. In addition, researchers are also interested in understanding which energy components are mostly affected by the mutation and how the mutation affects the overall structure of the corresponding protein. Here we report a webserver, the Single Amino Acid Mutation based change in Binding free Energy (SAAMBE) webserver, which addresses the demand for tools for predicting the change of protein binding free energy. SAAMBE is an easy to use webserver, which only requires that a coordinate file be inputted and the user is provided with various, but easy to navigate, options. The user specifies the mutation position, wild type residue and type of mutation to be made. The server predicts the binding free energy change, the changes of the corresponding energy components and provides the energy minimized 3D structure of the wild type and mutant proteins for download. The SAAMBE protocol performance was tested by benchmarking the predictions against over 1300 experimentally determined changes of binding free energy and a Pearson correlation coefficient of 0.62 was obtained. How the predictions can be used for discriminating disease-causing from harmless mutations is discussed. The webserver can be accessed via http://compbio.clemson.edu/saambe_webserver/.
Anon.
2013-06-15
After the events at the Japanese nuclear power plant of Fukushima Daiichi, the German Federal government decided that Germany will give up electricity generation from nuclear power within a decade. The last reactor will be disconnected from the power grid in 2022. Helping to make this opt-out safe is one of the duties of the Helmholtz Association with its Nuclear Safety Research Program within the Energy Research Area. Also the demolition of nuclear power plants and the repository problem will keep society, and thus also research, busy for a number of decades to come. Giving up electricity production from nuclear power thus must not mean giving up the required nuclear technology competences. In the fields of reactor safety, demolition, final storage, radiation protection, and crisis management, in critical support of international developments, and for competent evaluation of nuclear facilities around Germany, these competences will be in demand far beyond the German opt-out. This is the reason why the final report by the Ethics Committee on 'Safe Energy Supply' emphasizes the importance of nuclear technology research. Close cooperation on national, European and international levels is indispensable in this effort. Also nuclear safety research in the Helmholtz Association is aligned with the challenges posed by the opt-out of the use of nuclear power. It is important that the high competences in the areas of plant safety and demolition, handling of radioactive waste, and safe final storage as well as radiation protection be preserved. The Nuclear Safety Research Program within the Energy Research Area of the Helmholtz Association therefore will continue studying scientific and technical aspects of the safety of nuclear reactors and the safety of nuclear waste management. These research activities are provident research conducted for society and must be preserved for a long period of time. The work is closely harmonized with the activities of the partners
Chen, Changjun
2016-03-31
The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.
Minimum free-energy paths for the self-organization of polymer brushes.
Gleria, Ignacio; Mocskos, Esteban; Tagliazucchi, Mario
2017-03-22
A methodology to calculate minimum free-energy paths based on the combination of a molecular theory and the improved string method is introduced and applied to study the self-organization of polymer brushes under poor solvent conditions. Polymer brushes in a poor solvent cannot undergo macroscopic phase separation due to the physical constraint imposed by the grafting points; therefore, they microphase separate forming aggregates. Under some conditions, the theory predicts that the homogeneous brush and the aggregates can exist as two different minima of the free energy. The theoretical methodology introduced in this work allows us to predict the minimum free-energy path connecting these two minima as well as the morphology of the system along the path. It is shown that the transition between the homogeneous brush and the aggregates may involve a free-energy barrier or be barrierless depending on the relative stability of the two morphologies and the chain length and grafting density of the polymer. In the case where a free-energy barrier exists, one of the morphologies is a metastable structure and, therefore, the properties of the brush as the quality of the solvent is cycled are expected to display hysteresis. The theory is also applied to study the adhesion/deadhesion transition between two opposing surfaces modified by identical polymer brushes and it is shown that this process may also require surpassing a free-energy barrier.
Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions.
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.
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
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.
Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.
2017-10-01
Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.
Noise reduction efficiency of Helmholtz resonator in simulated channel of HVAC system
Hossein Ali Yousefi Rizi
2014-01-01
Conclusions: This research showed that the designed Helmholtz resonators at a certain frequency of low-frequency sound demonstrated the soundest decrease. The increase in the Helmholtz resonators′ chamber volume and their neck′s pass area are negatively associated with the rate of sound resonance. As a result, of determining the effective frequency range of the Helmholtz resonator, the designed resonator could be applied as an effective and efficient instrument of removing or decreasing noise.
Workman, Christopher; Krogh, Anders Stærmose
1999-01-01
This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly diff...
Towards abundant and pollution-free energy. Laser nuclear fusion
Robieux, J.
2008-01-01
This book shows that it is now practically certain that by the year 2080 laser nuclear fusion will allow to produce an abundant and relatively cheap energy. Thanks to this energy, it will be possible to convert a mixture of CO 2 , H 2 and water into an automotive fuel or a food product. Laser nuclear fusion will use deuterium as fuel and thus oil and gas will become useless. Also, thanks to this new energy source, global warming and starvation will be overcome. The laser fusion concept was introduced by J. Robieux in 1962 just after the discovery of the laser. This idea was immediately accepted and sustained by the French President De Gaulle. The research on laser fusion was initially undertaken at the Marcoussis research centre from the Compagnie Generale d'Electricite (General Electricity Company - CGE). In 1967, the lasers built at Marcoussis were 30 times more powerful than any other laser in the rest of world. A cooperation with the USA started at that time and is still going on today. In 1969, the CEA centre of Limeil realized the world premiere experiments of laser fusion. This book presents the historical aspects and the state-of-the-art of this technology today. It is written in two parts, the first part does not require any scientific knowledge and is accessible to everybody, while the second part can be understood only by readers having a basic scientific background. (J.S.)
Kjærgaard, Christian Hauge; Rossmeisl, Jan; Nørskov, Jens Kehlet
2010-01-01
In this paper, we present a method to directly compare the energy levels of intermediates in enzymatic and inorganic oxygen reduction catalysts. We initially describe how the energy levels of a Pt(111) catalyst, operating at pH = 0, are obtained. By a simple procedure, we then convert the energy...... levels of cytochrome c oxidase (CcO) models obtained at physiological pH = 7 to the energy levels at pH = 0, which allows for comparison. Furthermore, we illustrate how different bias voltages will affect the free-energy landscapes of the catalysts. This allows us to determine the so-called theoretical...
Interaction Free Energies of Eight Sodium Salts and a Phosphatidylcholine Membrane
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...
Analysis and control of a hybrid vehicle powered by free-piston energy converter
Hansson, Jörgen
2006-01-01
The introduction of hybrid powertrains has made it possible to utilise unconventional engines as primary power units in vehicles. The free-piston energy converter (FPEC) is such an engine. It is a combination of a free-piston combustion engine and a linear electrical machine. The main features of this configuration are high efficiency and a rapid transient response. In this thesis the free-piston energy converter as part of a hybrid powertrain is studied. One issue of the FPEC is the generati...
Stromberg, W H
1989-10-01
J. K. F. Zoellner began writing on "experimental proofs" of a fourth spatial dimension, and of the existence of spirits, in 1878. His arguments caused strong controversy, with rebuttal essays by Wilhelm Wundt and others. The author argues that Zoellner's case that these matters are experimental questions rested on arguments which Hermann von Helmholtz, inveighing against rationalist views of space and space perception, had recently published. Zoellner's use of Helmholtz's arguments to advance and defend his spiritist views occasioned strong criticism of Helmholtz, affected careers and reputations of scholars in Berlin and Leipzig, and caused enduring controversy over the credibility of Helmholtz's empiricist theory of space perception.
Effect of cold plasma on the Kelvin-Helmholtz instability
Melander, B.G.
1978-01-01
The thesis studies the effect of a two-component plasma (hot and cold) on the shear driven Kelvin-Helmholtz instability. An ion distribution with a shear flow parallel to the ambient magnetic field and a density gradient parallel to the shear direction is used. Both the electrostatic and electromagnetic versions of the instability are studied in the limit of hydromagnetic frequencies. The dispersion relation is obtained in the electrostatic case by solving the Vlasov equation for the perturbed ion and electron densities and then using the quasineutrality condition. In the electromagnetic case the coupled Vlasov and Maxwell's equations are solved to obtain the dispersion relation
Semi-analytic solution to planar Helmholtz equation
Tukač M.
2013-06-01
Full Text Available Acoustic solution of interior domains is of great interest. Solving acoustic pressure fields faster with lower computational requirements is demanded. A novel solution technique based on the analytic solution to the Helmholtz equation in rectangular domain is presented. This semi-analytic solution is compared with the finite element method, which is taken as the reference. Results show that presented method is as precise as the finite element method. As the semi-analytic method doesn’t require spatial discretization, it can be used for small and very large acoustic problems with the same computational costs.
Reconstruction of extended sources for the Helmholtz equation
Kress, Rainer; Rundell, William
2013-01-01
The basis of most imaging methods is to detect hidden obstacles or inclusions within a body when one can only make measurements on an exterior surface. Our underlying model is that of inverse acoustic scattering based on the Helmholtz equation. Our inclusions are interior forces with compact support and our data consist of a single measurement of near-field Cauchy data on the external boundary. We propose an algorithm that under certain assumptions allows for the determination of the support set of these forces by solving a simpler ‘equivalent point source’ problem, and which uses a Newton scheme to improve the corresponding initial approximation. (paper)
Black and gray Helmholtz-Kerr soliton refraction
Sanchez-Curto, Julio; Chamorro-Posada, Pedro; McDonald, Graham S.
2011-01-01
Refraction of black and gray solitons at boundaries separating different defocusing Kerr media is analyzed within a Helmholtz framework. A universal nonlinear Snell's law is derived that describes gray soliton refraction, in addition to capturing the behavior of bright and black Kerr solitons at interfaces. Key regimes, defined by beam and interface characteristics, are identified, and predictions are verified by full numerical simulations. The existence of a unique total nonrefraction angle for gray solitons is reported; both internal and external refraction at a single interface is shown possible (dependent only on incidence angle). This, in turn, leads to the proposal of positive or negative lensing operations on soliton arrays at planar boundaries.
Reconstruction of extended sources for the Helmholtz equation
Kress, Rainer
2013-02-26
The basis of most imaging methods is to detect hidden obstacles or inclusions within a body when one can only make measurements on an exterior surface. Our underlying model is that of inverse acoustic scattering based on the Helmholtz equation. Our inclusions are interior forces with compact support and our data consist of a single measurement of near-field Cauchy data on the external boundary. We propose an algorithm that under certain assumptions allows for the determination of the support set of these forces by solving a simpler \\'equivalent point source\\' problem, and which uses a Newton scheme to improve the corresponding initial approximation. © 2013 IOP Publishing Ltd.
Yang, Changwon; Kim, Eunae; Pak, Youngshang
2015-01-01
Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116
Yang, Changwon; Kim, Eunae; Pak, Youngshang
2015-09-18
Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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.
Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.
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.
Kaliakin, Danil S.; Zaari, Ryan R.; Varganov, Sergey A.
2015-01-01
Teaching fundamental physical chemistry concepts such as the potential energy surface, transition state, and reaction path is a challenging task. The traditionally used oversimplified 2D representation of potential and free energy surfaces makes this task even more difficult and often confuses students. We show how this 2D representation can be…
Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution
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.
Free energy and structure of dislocation cores in two-dimensional crystals
Bladon, P.B.; Frenkel, D.
2004-01-01
The nature of the melting transition in two dimensions is critically dependent on the core energy of dislocations. In this paper, we report calculations of the core free energy and the core size of dislocations in two-dimensional solids of systems interacting via square well, hard disk, and r-12
The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.
Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele
2017-09-14
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
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.
Computational scheme for pH-dependent binding free energy calculation with explicit solvent.
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.
Free Energy Self-Averaging in Protein-Sized Random Heteropolymers
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
Efficiency of free-energy calculations of spin lattices by spectral quantum algorithms
Master, Cyrus P.; Yamaguchi, Fumiko; Yamamoto, Yoshihisa
2003-01-01
Ensemble quantum algorithms are well suited to calculate estimates of the energy spectra for spin-lattice systems. Based on the phase estimation algorithm, these algorithms efficiently estimate discrete Fourier coefficients of the density of states. Their efficiency in calculating the free energy per spin of general spin lattices to bounded error is examined. We find that the number of Fourier components required to bound the error in the free energy due to the broadening of the density of states scales polynomially with the number of spins in the lattice. However, the precision with which the Fourier components must be calculated is found to be an exponential function of the system size
The evolution of a localized nonlinear wave of the Kelvin-Helmholtz instability with gravity
Orazzo, Annagrazia; Hoepffner, Jérôme
2012-11-01
At the interface between two fluids of different density and in the presence of gravity, there are well known periodic surface waves which can propagate for long distances with little attenuation, as it is for instance the case at the surface of the sea. If wind is present, these waves progressively accumulate energy as they propagate and grow to large sizes—this is the Kelvin-Helmholtz instability. On the other hand, we show in this paper that for a given wind strength, there is potential for the growth of a localized nonlinear wave. This wave can reach a size such that the hydrostatic pressure drop from top to bottom equals the stagnation pressure of the wind. This process for the disruption of the flat interface is localized and nonlinear. We study the properties of this wave using numerical simulations of the Navier-Stokes equations.
Kelvin-Helmholtz Instability: Lessons Learned and Ways Forward
Masson, A.; Nykyri, K.
2018-06-01
The Kelvin-Helmholtz instability (KHI) is a ubiquitous phenomenon across the Universe, observed from 500 m deep in the oceans on Earth to the Orion molecular cloud. Over the past two decades, several space missions have enabled a leap forward in our understanding of this phenomenon at the Earth's magnetopause. Key results obtained by these missions are first presented, with a special emphasis on Cluster and THEMIS. In particular, as an ideal instability, the KHI was not expected to produce mass transport. Simulations, later confirmed by spacecraft observations, indicate that plasma transport in Kelvin-Helmholtz (KH) vortices can arise during non-linear stage of its development via secondary process. In addition to plasma transport, spacecraft observations have revealed that KHI can also lead to significant ion heating due to enhanced ion-scale wave activity driven by the KHI. Finally, we describe what are the upcoming observational opportunities in 2018-2020, thanks to a unique constellation of multi-spacecraft missions including: MMS, Cluster, THEMIS, Van Allen Probes and Swarm.
The Common Data Acquisition Platform in the Helmholtz Association
Kaever, P.; Balzer, M.; Kopmann, A.; Zimmer, M.; Rongen, H.
2017-01-01
Various centres of the German Helmholtz Association (HGF) started in 2012 to develop a modular data acquisition (DAQ) platform, covering the entire range from detector readout to data transfer into parallel computing environments. This platform integrates generic hardware components like the multi-purpose HGF-Advanced Mezzanine Card or a smart scientific camera framework, adding user value with Linux drivers and board support packages. Technically the scope comprises the DAQ-chain from FPGA-modules to computing servers, notably frontend-electronics-interfaces, microcontrollers and GPUs with their software plus high-performance data transmission links. The core idea is a generic and component-based approach, enabling the implementation of specific experiment requirements with low effort. This so called DTS-platform will support standards like MTCA.4 in hard- and software to ensure compatibility with commercial components. Its capability to deploy on other crate standards or FPGA-boards with PCI express or Ethernet interfaces remains an essential feature. Competences of the participating centres are coordinated in order to provide a solid technological basis for both research topics in the Helmholtz Programme ''Matter and Technology'': ''Detector Technology and Systems'' and ''Accelerator Research and Development''. The DTS-platform aims at reducing costs and development time and will ensure access to latest technologies for the collaboration. Due to its flexible approach, it has the potential to be applied in other scientific programs.
The Common Data Acquisition Platform in the Helmholtz Association
Kaever, P.; Balzer, M.; Kopmann, A.; Zimmer, M.; Rongen, H.
2017-04-01
Various centres of the German Helmholtz Association (HGF) started in 2012 to develop a modular data acquisition (DAQ) platform, covering the entire range from detector readout to data transfer into parallel computing environments. This platform integrates generic hardware components like the multi-purpose HGF-Advanced Mezzanine Card or a smart scientific camera framework, adding user value with Linux drivers and board support packages. Technically the scope comprises the DAQ-chain from FPGA-modules to computing servers, notably frontend-electronics-interfaces, microcontrollers and GPUs with their software plus high-performance data transmission links. The core idea is a generic and component-based approach, enabling the implementation of specific experiment requirements with low effort. This so called DTS-platform will support standards like MTCA.4 in hard- and software to ensure compatibility with commercial components. Its capability to deploy on other crate standards or FPGA-boards with PCI express or Ethernet interfaces remains an essential feature. Competences of the participating centres are coordinated in order to provide a solid technological basis for both research topics in the Helmholtz Programme ``Matter and Technology'': ``Detector Technology and Systems'' and ``Accelerator Research and Development''. The DTS-platform aims at reducing costs and development time and will ensure access to latest technologies for the collaboration. Due to its flexible approach, it has the potential to be applied in other scientific programs.
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 minimization to predict RNA secondary structures and computational RNA design.
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.
Free Radicals and Antioxidant Status in Protein Energy Malnutrition
M. Khare
2014-01-01
Full Text Available Background/Objectives. The aim of this study was to evaluate oxidant and antioxidant status in children with different grades of Protein Energy Malnutrition (PEM. Subjects/Methods. A total of two hundred fifty (250 children (age range: 6 months to 5 years living in eastern UP, India, were recruited. One hundred and ninety-three (193 of these children had different grades of PEM (sixty-five (65 children belong to mild, sixty (60 to moderate, and sixty-eight (68 to severe group. Grading in group was done after standardization in weight and height measurements. Fifty-seven (57 children who are age and and sex matched, healthy, and well-nourished were recruited from the local community and used as controls after checking their protein status (clinical nutritional status with height and weight standardization. Redox homeostasis was assessed using spectrophotometric/colorimetric methods. Results. In our study, erythrocyte glutathione (GSH, plasma Cu, Zn-superoxide dismutase (Cu,Zn-SOD,EC 1.15.1.1, ceruloplasmin (Cp, and ascorbic acid were significantly (P<0.001 more decreased in children with malnutrition than controls. Plasma malondialdehyde (MDA, and protein carbonyl (PC were significantly (P<0.001 raised in cases as compared to controls. Conclusion. Stress is created as a result of PEM which is responsible for the overproduction of reactive oxygen species (ROSs. These ROSs will lead to membrane oxidation and thus an increase in lipid peroxidation byproducts such as MDA and protein oxidation byproducts such as PC mainly. Decrease in level of antioxidants suggests an increased defense against oxidant damage. Changes in oxidant and antioxidant levels may be responsible for grading in PEM.
Nagura, Yuko; Tsujimoto, Akimasa; Barkmeier, Wayne W; Watanabe, Hidehiko; Johnson, William W; Takamizawa, Toshiki; Latta, Mark A; Miyazaki, Masashi
2018-04-01
The relationship between enamel bond fatigue durability and surface free-energy characteristics with universal adhesives was investigated. The initial shear bond strengths and shear fatigue strengths of five universal adhesives to enamel were determined with and without phosphoric acid pre-etching. The surface free-energy characteristics of adhesive-treated enamel with and without pre-etching were also determined. The initial shear bond strength and shear fatigue strength of universal adhesive to pre-etched enamel were higher than those to ground enamel. The initial shear bond strength and shear fatigue strength of universal adhesive to pre-etched enamel were material dependent, unlike those to ground enamel. The surface free-energy of the solid (γ S ) and the hydrogen-bonding force (γSh) of universal adhesive-treated enamel were different depending on the adhesive, regardless of the presence or absence of pre-etching. The bond fatigue durability of universal adhesives was higher to pre-etched enamel than to ground enamel. In addition, the bond fatigue durability to pre-etched enamel was material dependent, unlike that to ground enamel. The surface free-energy characteristics of universal adhesive-treated enamel were influenced by the adhesive type, regardless of the presence or absence of pre-etching. The surface free-energy characteristics of universal adhesive-treated enamel were related to the results of the bond fatigue durability. © 2018 Eur J Oral Sci.
Prior Flaring as a Complement to Free Magnetic Energy for Forecasting Solar Eruptions
Falconer, David A.; Moore, Ronald L.; Barghouty, Abdulnasser F.; Khazanov, Igor
2012-01-01
From a large database of (1) 40,000 SOHO/MDI line-of-sight magnetograms covering the passage of 1,300 sunspot active regions across the 30 deg radius central disk of the Sun, (2) a proxy of each active region's free magnetic energy measured from each of the active region's central-disk-passage magnetograms, and (3) each active region's full-disk-passage history of production of major flares and fast coronal mass ejections (CMEs), we find new statistical evidence that (1) there are aspects of an active region's magnetic field other than the free energy that are strong determinants of the active region's productivity of major flares and fast CMEs in the coming few days, (2) an active region's recent productivity of major flares, in addition to reflecting the amount of free energy in the active region, also reflects these other determinants of coming productivity of major eruptions, and (3) consequently, the knowledge of whether an active region has recently had a major flare, used in combination with the active region's free-energy proxy measured from a magnetogram, can greatly alter the forecast chance that the active region will have a major eruption in the next few days after the time of the magnetogram. The active-region magnetic conditions that, in addition to the free energy, are reflected by recent major flaring are presumably the complexity and evolution of the field.
Koji Ogata
2018-02-01
Full Text Available The octanol–water partition coefficient (logPow is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values.
Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L
2016-01-01
Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. © 2016 Elsevier Inc. All rights reserved.
PRIOR FLARING AS A COMPLEMENT TO FREE MAGNETIC ENERGY FOR FORECASTING SOLAR ERUPTIONS
Falconer, David A.; Moore, Ronald L.; Barghouty, Abdulnasser F.; Khazanov, Igor
2012-01-01
From a large database of (1) 40,000 SOHO/MDI line-of-sight magnetograms covering the passage of 1300 sunspot active regions across the 30° radius central disk of the Sun, (2) a proxy of each active region's free magnetic energy measured from each of the active region's central-disk-passage magnetograms, and (3) each active region's full-disk-passage history of production of major flares and fast coronal mass ejections (CMEs), we find new statistical evidence that (1) there are aspects of an active region's magnetic field other than the free energy that are strong determinants of the active region's productivity of major flares and fast CMEs in the coming few days; (2) an active region's recent productivity of major flares, in addition to reflecting the amount of free energy in the active region, also reflects these other determinants of coming productivity of major eruptions; and (3) consequently, the knowledge of whether an active region has recently had a major flare, used in combination with the active region's free-energy proxy measured from a magnetogram, can greatly alter the forecast chance that the active region will have a major eruption in the next few days after the time of the magnetogram. The active-region magnetic conditions that, in addition to the free energy, are reflected by recent major flaring are presumably the complexity and evolution of the field.
AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.
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.
BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.
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.
Ngo, Son Tung; Mai, Binh Khanh; Hiep, Dinh Minh; Li, Mai Suan
2015-10-01
The binding mechanism of AC1NX476 to HIV-1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free energy was calculated using the double-annihilation binding free energy method. It is shown that the binding affinity of AC1NX476 to wild type is higher than not only ritonavir but also darunavir, making AC1NX476 become attractive candidate for HIV treatment. Our theoretical results are in excellent agreement with the experimental data as the correlation coefficient between calculated and experimentally measured binding free energies R = 0.993. Residues Asp25-A, Asp29-A, Asp30-A, Ile47-A, Gly48-A, and Val50-A from chain A, and Asp25-B from chain B play a crucial role in the ligand binding. The mutations were found to reduce the receptor-ligand interaction by widening the binding cavity, and the binding propensity is mainly driven by the van der Waals interaction. Our finding may be useful for designing potential drugs to combat with HIV. © 2015 John Wiley & Sons A/S.
Lee, Geun Woo; Jeon, Sangho; Park, Cheolmin; Kang, Dong-Hee
2013-01-01
Highlights: • Thermophysical properties of liquid Ti are obtained by electrostatic levitation. • How to measure the thermophysical properties is shown with non-contact method. • Hypercooling limit of liquid Ti guarantying homogeneous nucleation is 341 K. • Accurate ratio C p /ε T of the liquid Ti is obtained with weak temperature dependence. • Interfacial free energy of Ti is estimated with the thermophysical parameters. -- Abstract: Thermophysical properties of liquid Ti are measured by a newly developed electrostatic levitation. In this study, we measure a hypercooling limit (ΔT hyp ), specific heat (C p ), total hemispherical emissivity (ε T ), and density (ρ) of liquid Ti. The ΔT hyp of the liquid Ti is 341 K. The C p of the liquid Ti shows very weak temperature dependence during supercooling. The ε T and ρ of the liquid Ti are given by 0.329 and ρ(T) (g/cm 3 ) = (4.16 − 2.36) · 10 −4 (T − T m ). Finally, the interfacial free energy is estimated with the measured thermophysical parameters. The interfacial free energy is 0.164 J/m 2 , and Turnbull’s coefficient is 0.48
Transmission problems for the Helmholtz equation for a rectilinear-circular lune
Volodymyr Denysenko
2007-01-01
Full Text Available The question related to the construction of the solution of plane transmission problem for the Helmholtz equation in a rectilinear-circular lune is considered. An approach is proposed based on the method of partial domains and the principle of reflection for the solutions of the Helmholtz equation through the segment.
Fast exploration of an optimal path on the multidimensional free energy surface
Chen, Changjun
2017-01-01
In a reaction, determination of an optimal path with a high reaction rate (or a low free energy barrier) is important for the study of the reaction mechanism. This is a complicated problem that involves lots of degrees of freedom. For simple models, one can build an initial path in the collective variable space by the interpolation method first and then update the whole path constantly in the optimization. However, such interpolation method could be risky in the high dimensional space for large molecules. On the path, steric clashes between neighboring atoms could cause extremely high energy barriers and thus fail the optimization. Moreover, performing simulations for all the snapshots on the path is also time-consuming. In this paper, we build and optimize the path by a growing method on the free energy surface. The method grows a path from the reactant and extends its length in the collective variable space step by step. The growing direction is determined by both the free energy gradient at the end of the path and the direction vector pointing at the product. With fewer snapshots on the path, this strategy can let the path avoid the high energy states in the growing process and save the precious simulation time at each iteration step. Applications show that the presented method is efficient enough to produce optimal paths on either the two-dimensional or the twelve-dimensional free energy surfaces of different small molecules. PMID:28542475
Structure-based prediction of free energy changes of binding of PTP1B inhibitors
Wang, Jing; Ling Chan, Shek; Ramnarayan, Kal
2003-08-01
The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.
Casimir free energy of dielectric films: classical limit, low-temperature behavior and control.
Klimchitskaya, G L; Mostepanenko, V M
2017-07-12
The Casimir free energy of dielectric films, both free-standing in vacuum and deposited on metallic or dielectric plates, is investigated. It is shown that the values of the free energy depend considerably on whether the calculation approach used neglects or takes into account the dc conductivity of film material. We demonstrate that there are material-dependent and universal classical limits in the former and latter cases, respectively. The analytic behavior of the Casimir free energy and entropy for a free-standing dielectric film at low temperature is found. According to our results, the Casimir entropy goes to zero when the temperature vanishes if the calculation approach with neglected dc conductivity of a film is employed. If the dc conductivity is taken into account, the Casimir entropy takes the positive value at zero temperature, depending on the parameters of a film, i.e. the Nernst heat theorem is violated. By considering the Casimir free energy of SiO 2 and Al 2 O 3 films deposited on a Au plate in the framework of two calculation approaches, we argue that physically correct values are obtained by disregarding the role of dc conductivity. A comparison with the well known results for the configuration of two parallel plates is made. Finally, we compute the Casimir free energy of SiO 2 , Al 2 O 3 and Ge films deposited on high-resistivity Si plates of different thicknesses and demonstrate that it can be positive, negative and equal to zero. The effect of illumination of a Si plate with laser light is considered. Possible applications of the obtained results to thin films used in microelectronics are discussed.
Casimir free energy of dielectric films: classical limit, low-temperature behavior and control
Klimchitskaya, G. L.; Mostepanenko, V. M.
2017-07-01
The Casimir free energy of dielectric films, both free-standing in vacuum and deposited on metallic or dielectric plates, is investigated. It is shown that the values of the free energy depend considerably on whether the calculation approach used neglects or takes into account the dc conductivity of film material. We demonstrate that there are material-dependent and universal classical limits in the former and latter cases, respectively. The analytic behavior of the Casimir free energy and entropy for a free-standing dielectric film at low temperature is found. According to our results, the Casimir entropy goes to zero when the temperature vanishes if the calculation approach with neglected dc conductivity of a film is employed. If the dc conductivity is taken into account, the Casimir entropy takes the positive value at zero temperature, depending on the parameters of a film, i.e. the Nernst heat theorem is violated. By considering the Casimir free energy of SiO2 and Al2O3 films deposited on a Au plate in the framework of two calculation approaches, we argue that physically correct values are obtained by disregarding the role of dc conductivity. A comparison with the well known results for the configuration of two parallel plates is made. Finally, we compute the Casimir free energy of SiO2, Al2O3 and Ge films deposited on high-resistivity Si plates of different thicknesses and demonstrate that it can be positive, negative and equal to zero. The effect of illumination of a Si plate with laser light is considered. Possible applications of the obtained results to thin films used in microelectronics are discussed.
Free energy and plaquette expectation value for gluons on the lattice, in three dimensions
Panagopoulos, H.; Skouroupathis, A.; Tsapalis, A.
2006-01-01
We calculate the perturbative value of the free energy in lattice QCD in three dimensions, up to three loops. Our calculation is performed using the Wilson formulation for gluons in SU(N) gauge theories. The free energy is directly related to the average plaquette. To carry out the calculation, we compute the coefficients involved in the perturbative expansion of the Free Energy up to three loops, using an automated set of procedures developed by us in Mathematica. The dependence on N is shown explicitly in our results. For purposes of comparison, we also present the individual contributions from every diagram. These have been obtained by means of two independent calculations, in order to cross check our results
Absolute Hydration Free Energy of Proton from First Principles Electronic Structure Calculations
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+)
The vortex free energy in the screening phase of the Z(2) Higgs model
Meyer, H.
1983-06-01
The vortex free energy was proposed to distinguish between the confinement - and the Higgs phase (in the sense of 't Hooft) in lattice gauge theory, when matter fields are present that transform according to an arbitrary representation of the gauge group. In this paper I consider the Z(2) Higgs model and calculate the vortex free energy in the screening part of the confining/screening phase of Fradkin and Shenker. The result does not agree with the expected behavior that corresponds to the structure of the phase diagram. Therefore the vortex free energy is no longer a good indicator for confinement when matter fields transform nontrivially under the center of the gauge group (such as Z(2) Higgs scalars). (orig.)
Free energy calculations along entropic pathways. III. Nucleation of capillary bridges and bubbles
Desgranges, Caroline; Delhommelle, Jerome
2017-05-01
Using molecular simulation, we analyze the capillary condensation and evaporation processes for argon confined in a cylindrical nanopore. For this purpose, we define the entropy of the adsorbed fluid as a reaction coordinate and determine the free energy associated with both processes along entropic pathways. For capillary condensation, we identify a complex free energy profile resulting from the multi-stage nature of this phenomenon. We find capillary condensation to proceed through the nucleation of a liquid bridge across the nanopore, followed by its expansion throughout the pore to give rise to the stable phase of high density. In the case of capillary evaporation, the free energy profile along the entropy pathway also exhibits different regimes, corresponding to the initial destabilization of the layered structure of the fluid followed by the formation, and subsequent expansion, of a bubble across the nanopore.
Tremaine, P.R.
1979-01-01
Methods for calculating high-temprature Gibbs free energies of mononuclear cations and anions from room-temperature data are reviewed. Emphasis is given to species required for oxide solubility calculations relevant to mass transport situations in the nuclear industry. Free energies predicted by each method are compared to selected values calculated from recently reported solubility studies and other literature data. Values for monatomic ions estimated using the assumption anti C 0 p(T) = anti C 0 p(298) agree best with experiment to 423 K. From 423 K to 523 K, free energies from an electrostatic model for ion hydration are more accurate. Extrapolations for hydrolyzed species are limited by a lack of room-temperature entropy data and expressions for estimating these entropies are discussed. (orig.) [de
Control of the Effective Free-Energy Landscape in a Frustrated Magnet by a Field Pulse
Wan, Yuan; Moessner, Roderich
2017-10-01
Thermal fluctuations can lift the degeneracy of a ground state manifold, producing a free-energy landscape without accidentally degenerate minima. In a process known as order by disorder, a subset of states incorporating symmetry breaking may be selected. Here, we show that such a free-energy landscape can be controlled in a nonequilibrium setting as the slow motion within the ground state manifold is governed by the fast modes out of it. For the paradigmatic case of the classical pyrochlore X Y antiferromagnet, we show that a uniform magnetic field pulse can excite these fast modes to generate a tunable effective free-energy landscape with minima at thermodynamically unstable portions of the ground state manifold.
Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections; TOPICAL
G.S. Choe; C.Z. Cheng
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
Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections
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
Modeling free energy availability from Hadean hydrothermal systems to the first metabolism.
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.
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.
Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics
Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.
2015-12-01
Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.
Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics
Lau, Gabriel V.; Müller, Erich A.; Jackson, George [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Hunt, Patricia A. [Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Ford, Ian J. [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom)
2015-12-28
Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.
Can the regulated market help foster a free market for wind energy in Brazil?
Dalbem, Marta Corrêa; Brandão, Luiz Eduardo Teixeira; Gomes, Leonardo Lima
2014-01-01
Wind energy has been negotiated in Brazil's regulated market through auctions organized by the government. Bilateral negotiations in the free market have been scarce. In 2011 wind farms were allowed to bid in ‘A minus 5 (A−5)' auctions, for energy with first delivery date 5 years ahead. This new design was expected to stimulate negotiations in the free market, as the 20-year contract in the regulated market eases financing while the 5-year grace period grants wind farms the option to sell whatever energy is generated beforehand in the free market. We modeled bidders' price decision in A−5 auctions as Real Options and concluded that given the low prices averaging USD 50/MW h, winners are tempted to defer investment, expecting more favorable equipment and energy prices, or a better knowledge of the wind site. Construction is likely to begin in 2–3 years, with little time left for the free market. Bidders that consider the option of eventually abandoning the project are more price competitive, increasing chances that some wind farms will never materialize. Therefore, this attempt to foster the free market may not pay-off and, moreover, it may have the unfavorable effect of turning Brazil's energy expansion planning a more difficult task. - Highlights: • Tight auction prices make winners exercise options to defer construction. • Investors that consider the option to abandon the project tend to win the auction. • High chances of default, when investors take abandonment options into account. • Auctioning wind farms for energy delivery 5 yr later will not foster a free market
Merging Belief Propagation and the Mean Field Approximation: A Free Energy Approach
Riegler, Erwin; Kirkelund, Gunvor Elisabeth; Manchón, Carles Navarro
2013-01-01
We present a joint message passing approach that combines belief propagation and the mean field approximation. Our analysis is based on the region-based free energy approximation method proposed by Yedidia et al. We show that the message passing fixed-point equations obtained with this combination...... correspond to stationary points of a constrained region-based free energy approximation. Moreover, we present a convergent implementation of these message passing fixed-point equations provided that the underlying factor graph fulfills certain technical conditions. In addition, we show how to include hard...
Combined production of free-range pigs and energy crops – animal behaviour and crop damages
Horsted, Klaus; Kongsted, Anne Grete; Jørgensen, Uffe
2012-01-01
Intensive free-range pig production on open grasslands has disadvantages in that it creates nutrient hotspots and little opportunity for pigs to seek shelter from the sun. Combining a perennial energy crop and pig production might benefit the environment and animal welfare because perennial energy...... crops like willow (Salix sp.) and Miscanthus offer the pigs protection from the sun while reducing nutrient leaching from pig excrements due to their deep rooting system. The objectives of this study were to evaluate how season and stocking density of pigs in a free-range system with zones of willow...
Polymer in a pore: Effect of confinement on the free energy barrier
Kumar, Sanjiv; Kumar, Sanjay
2018-06-01
We investigate the transfer of a polymer chain from cis- side to trans- side through two types of pores: cone-shaped channel and flat-channel. Using the exact enumeration technique, we obtain the free energy landscapes of a polymer chain for such systems. We have also calculated the free-energy barrier of a polymer chain attached to the edge of the pore. The model system allows us to calculate the force required to pull polymer from the pore and stall-force to confine polymer within the pore.
Development of a Miniature, Two-Axis, Triple-Helmholtz-Driven Gimbal
Sharif, Boz; Joscelyn, Ed; Wilcox, Brian; Johnson, Michael R.
2000-01-01
This paper details the development of a Helmholtz-driven, 2-axis gimbal to position a flat mirror within 50 microradian (fine positioning) in a space environment. The gimbal is intended to travel on a deep space mission mounted on a miniature "rover" vehicle. The gimbal will perform both pointing and scanning functions. The goal for total mass of the gimbal was 25 grams. The primary challenge was to design and build a bearing system that would achieve the required accuracy in addition to supporting the relatively large mass of the mirror and the outer gimbal. The mechanism is subjected to 100-G loading without the aid of any additional caging mechanism. Additionally, it was desired to have the same level of accuracy during Earth-bound, 1-G testing. Due to the inherent lack of damping in a zero-G, vacuum environment; the ability of the gimbal to respond to very small amounts of input energy is paramount. Initial testing of the first prototype revealed exceedingly long damping times required even while exposed to the damping effects of air and 1-G friction. It is envisioned that fine positioning of the gimbal will be accomplished in very small steps to avoid large disturbances to the mirror. Various bearing designs, including materials, lubrication options and bearing geometry will be discussed. In addition various options for the Helmholtz coil design will be explored with specific test data given. Ground testing in the presence of 1-G was compounded by the local magnetic fields due to the "compass" effect on the gimbal. The test data will be presented and discussed. Additionally, rationale for estimating gimbal performance in a zero-G environment will be presented and discussed.
Acoustic response of Helmholtz dampers in the presence of hot grazing flow
Ćosić, B.; Wassmer, D.; Terhaar, S.; Paschereit, C. O.
2015-01-01
Thermoacoustic instabilities are high amplitude instabilities of premixed gas turbine combustors. Cooled passive dampers are used to attenuate or suppress these instabilities in the combustion chamber. For the first time, the influence of temperature differences between the grazing flow in the combustor and the cross-flow emanating from the Helmholtz damper is comprehensively investigated in the linear and nonlinear amplitude regime. The flow field inside the resonator and in the vicinity of the neck is measured with high-speed particle image velocimetry for various amplitudes and at different momentum-flux ratios of grazing and purging flow. Seeding is used as a tracer to qualitatively assess the mixing of the grazing and purging flow as well as the ingestion into the neck of the resonator. Experimentally, the acoustic response for various temperature differences between grazing and purging flow is investigated. The multi-microphone method, in combination with two microphones flush-mounted in the resonator volume and two microphones in the plane of the resonator entrance, is used to determine the impedance of the Helmholtz resonator in the linear and nonlinear amplitude regime for various temperatures and different momentum-flux ratios. Additionally, a thermocouple was used to measure the temperature in the neck. The acoustic response and the temperature measurements are used to obtain the virtual neck length and the effective area jump from a detailed impedance model. This model is extended to include the observed acoustic energy dissipation caused by the density gradients at the neck vicinity. A clear correlation between temperature differences and changes of the mass end-correction is confirmed. The capabilities of the impedance model are demonstrated.
Sokaogon Chippewa Community Emission-Free and Treaty Resource Protection Clean Energy Initiative
Quade, Ron
2018-03-30
Final Report for DOE project DE-IE0000036 The Sokaogon Chippewa Community received a tribal clean energy initiative grant and installed a community wide solar system estimated to produce 606 kw of carbon free clean energy on seventeen (17) tribal buildings and three (3) residential homes significantly reducing the tribes’ energy bills over the life of the system, potentially saving the tribe up to $2.7 million in energy savings over a thirty (30) year time span. Fifteen (15) solar installations utilized aluminum roof-top mounting systems while two (2) installations utilized a ground mount aluminum racking system.
Yan, Yaming; Song, Linze; Shi, Qiang
2018-02-28
By employing several lattice model systems, we investigate the free energy barrier and real-time dynamics of charge separation in organic photovoltaic (OPV) cells. It is found that the combined effects of the external electric field, entropy, and charge delocalization reduce the free energy barrier significantly. The dynamic disorder reduces charge carrier delocalization and results in the increased charge separation barrier, while the effect of static disorder is more complicated. Simulation of the real-time dynamics indicates that the free charge generation process involves multiple time scales, including an ultrafast component within hundreds of femtoseconds, an intermediate component related to the relaxation of the hot charge transfer (CT) state, and a slow component on the time scale of tens of picoseconds from the thermally equilibrated CT state. Effects of hot exciton dissociation as well as its dependence on the energy offset between the Frenkel exciton and the CT state are also analyzed. The current results indicate that only a small energy offset between the band gap and the lowest energy CT state is needed to achieve efficient free charge generation in OPV devices, which agrees with recent experimental findings.
Yan, Yaming; Song, Linze; Shi, Qiang
2018-02-01
By employing several lattice model systems, we investigate the free energy barrier and real-time dynamics of charge separation in organic photovoltaic (OPV) cells. It is found that the combined effects of the external electric field, entropy, and charge delocalization reduce the free energy barrier significantly. The dynamic disorder reduces charge carrier delocalization and results in the increased charge separation barrier, while the effect of static disorder is more complicated. Simulation of the real-time dynamics indicates that the free charge generation process involves multiple time scales, including an ultrafast component within hundreds of femtoseconds, an intermediate component related to the relaxation of the hot charge transfer (CT) state, and a slow component on the time scale of tens of picoseconds from the thermally equilibrated CT state. Effects of hot exciton dissociation as well as its dependence on the energy offset between the Frenkel exciton and the CT state are also analyzed. The current results indicate that only a small energy offset between the band gap and the lowest energy CT state is needed to achieve efficient free charge generation in OPV devices, which agrees with recent experimental findings.
Shi, Frank G.
1994-01-01
A method is introduced to measure the free-energy barrier W(sup *), the activation energy, and activation entropy to nucleation of crystallites in amorphous solids, independent of the energy barrier to growth. The method allows one to determine the temperature dependence of W(sup *), and the effect of the preparation conditions of the initial amorphous phase, the dopants, and the crystallization methds on W(sup *). The method is applied to determine the free-energy barrier to nucleation of crystallites in amorphous silicon (a-Si) thin films. For thermally induced nucleation in a-Si thin films with annealing temperatures in the range of from 824 to 983 K, the free-energy barrier W(sup *) to nucleation of silicon crystals is about 2.0 - 2.1 eV regardless of the preparation conditions of the films. The observation supports the idea that a-Si transforms into an intermediate amorphous state through the structural relaxation prior to the onset of nucleation of crystallites in a-Si. The observation also indicates that the activation entropy may be an insignificant part of the free-energy barrier for the nucleation of crystallites in a-Si. Compared with the free-energy barrier to nucleation of crystallites in undoped a-Si films, a significant reduction is observed in the free-energy barrier to nucleation in Cu-doped a-Si films. For a-Si under irradiation of Xe(2+) at 10(exp 5) eV, the free-energy barrier to ion-induced nucleation of crystallites is shown to be about half of the value associated with thermal-induced nucleation of crystallites in a-Si under the otherwise same conditions, which is much more significant than previously expected. The present method has a general kinetic basis; it thus should be equally applicable to nucleation of crystallites in any amorphous elemental semiconductors and semiconductor alloys, metallic and polymeric glasses, and to nucleation of crystallites in melts and solutions.
A Parallel Sweeping Preconditioner for Heterogeneous 3D Helmholtz Equations
Poulson, Jack
2013-05-02
A parallelization of a sweeping preconditioner for three-dimensional Helmholtz equations without large cavities is introduced and benchmarked for several challenging velocity models. The setup and application costs of the sequential preconditioner are shown to be O(γ2N4/3) and O(γN logN), where γ(ω) denotes the modestly frequency-dependent number of grid points per perfectly matched layer. Several computational and memory improvements are introduced relative to using black-box sparse-direct solvers for the auxiliary problems, and competitive runtimes and iteration counts are reported for high-frequency problems distributed over thousands of cores. Two open-source packages are released along with this paper: Parallel Sweeping Preconditioner (PSP) and the underlying distributed multifrontal solver, Clique. © 2013 Society for Industrial and Applied Mathematics.
The Kelvin-Helmholtz instability on the magnetopause
Kivelson, M.G.; California Univ., Los Angeles; Pu, Z.-Y.
1984-01-01
Conditions for the development of Kelvin-Helmholtz (K-H) waves on the magnetopause have been known for more than 15 years; more recently, spacecraft observations have stimulated further examination of the properties of K-H waves. For a magnetopause with no boundary layer, two different modes of surface waves have been identified and their properties have been investigated for various assumed orientations of magnetic field and flow velocity vectors. The power radiated into the magnetosphere from the velocity shear at the boundary has been estimated. Other calculations have focused on the consequences of finite thickness boundary layers, both uniform and non-uniform. The boundary layer is found to modify the wave modes present at the magnetopause and to yield a criterion for the wavelength of the fastest growing surface waves. The paper concludes by questioning the extent to which the inferences from boundary layer models are model dependent and identifies areas where further work is needed or anticipated. (author)
Integrability and symmetries for the Helmholtz oscillator with friction
Almendral, Juan A; Sanjuan, Miguel A F
2003-01-01
This paper deals with the Helmholtz oscillator, which is a simple nonlinear oscillator whose equation presents a quadratic nonlinearity and the possibility of escape. When a periodic external force is introduced, the width of the stochastic layer, which is a region around the separatrix where orbits may exhibit transient chaos, is calculated. In the absence of friction and external force, it is well known that analytical solutions exist since it is completely integrable. When only friction is included, there is no analytical solution for all parameter values. However, by means of the Lie theory for differential equations we find a relation between parameters for which the oscillator is integrable. This is related to the fact that the system possesses a symmetry group and the corresponding symmetries are computed. Finally, the analytical explicit solutions are shown and related to the basins of attraction
Efficient approach to obtain free energy gradient using QM/MM MD simulation
Asada, Toshio; Koseki, Shiro; Ando, Kanta
2015-01-01
The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method
Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.
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.
The Maximum Free Magnetic Energy Allowed in a Solar Active Region
Moore, Ronald L.; Falconer, David A.
2009-01-01
Two whole-active-region magnetic quantities that can be measured from a line-of-sight magnetogram are (sup L) WL(sub SG), a gauge of the total free energy in an active region's magnetic field, and sup L(sub theta), a measure of the active region's total magnetic flux. From these two quantities measured from 1865 SOHO/MDI magnetograms that tracked 44 sunspot active regions across the 0.5 R(sub Sun) central disk, together with each active region's observed production of CMEs, X flares, and M flares, Falconer et al (2009, ApJ, submitted) found that (1) active regions have a maximum attainable free magnetic energy that increases with the magnetic size (sup L) (sub theta) of the active region, (2) in (Log (sup L)WL(sub SG), Log(sup L) theta) space, CME/flare-productive active regions are concentrated in a straight-line main sequence along which the free magnetic energy is near its upper limit, and (3) X and M flares are restricted to large active regions. Here, from (a) these results, (b) the observation that even the greatest X flares produce at most only subtle changes in active region magnetograms, and (c) measurements from MSFC vector magnetograms and from MDI line-of-sight magnetograms showing that practically all sunspot active regions have nearly the same area-averaged magnetic field strength: =- theta/A approximately equal to 300 G, where theta is the active region's total photospheric flux of field stronger than 100 G and A is the area of that flux, we infer that (1) the maximum allowed ratio of an active region's free magnetic energy to its potential-field energy is 1, and (2) any one CME/flare eruption releases no more than a small fraction (less than 10%) of the active region's free magnetic energy. This work was funded by NASA's Heliophysics Division and NSF's Division of Atmospheric Sciences.
Evaluation of the accuracy of the free-energy-minimization method
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
Anuruddh Kumar
2014-06-01
Full Text Available In this article, the performance of various piezoelectric materials is simulated for the unimorph cantilever-type piezoelectric energy harvester. The finite element method (FEM is used to model the piezolaminated unimorph cantilever structure. The first-order shear deformation theory (FSDT and linear piezoelectric theory are implemented in finite element simulations. The genetic algorithm (GA optimization approach is carried out to optimize the structural parameters of mechanical energy-based energy harvester for maximum power density and power output. The numerical simulation demonstrates the performance of lead-free piezoelectric materials in unimorph cantilever-based energy harvester. The lead-free piezoelectric material K0.5Na0.5NbO3-LiSbO3-CaTiO3 (2 wt.% has demonstrated maximum mean power and maximum mean power density for piezoelectric energy harvester in the ambient frequency range of 90–110 Hz. Overall, the lead-free piezoelectric materials of K0.5Na0.5NbO3-LiSbO3 (KNN-LS family have shown better performance than the conventional lead-based piezoelectric material lead zirconate titanate (PZT in the context of piezoelectric energy harvesting devices.
Prediction of the metabolizable energy requirements of free-range laying hens.
Brainer, M M A; Rabello, C B V; Santos, M J B; Lopes, C C; Ludke, J V; Silva, J H V; Lima, R A
2016-01-01
This experiment was conducted with the aim of estimating the ME requirements of free-range laying hens for maintenance, weight gain, and egg production. These experiments were performed to develop an energy requirement prediction equation by using the comparative slaughter technique and the total excreta collection method. Regression equations were used to relate the energy intake, the energy retained in the body and eggs, and the heat production of the hens. These relationships were used to determine the daily ME requirement for maintenance, the efficiency energy utilization above the requirements for maintenance, and the NE requirement for maintenance. The requirement for weight gain was estimated from the energy content of the carcass, and the diet's efficiency energy utilization was determined from the weight gain, which was measured during weekly slaughter. The requirement for egg production was estimated by considering the energy content of the eggs and the efficiency of energy deposition in the eggs. The requirement and efficiency energy utilization for maintenance were 121.8 kcal ME/(kg∙d)and 0.68, respectively. Similarly, the NE requirement for maintenance was 82.4 kcal ME/(kg∙d), and the efficiency energy utilization above maintenance was 0.61. Because the carcass body weight and energy did not increase during the trial, the weight gain could not be estimated. The requirements for egg production requirement and efficiency energy utilization for egg production were 2.48 kcal/g and 0.61, respectively. The following energy prediction equation for free-range laying hens (without weight gain) was developed: ME /(hen ∙ d) = 121.8 × W + 2.48 × EM, in which W = body weight (kg) and EM = egg mass (g/[hen ∙ d]).
Collision-Free Structure Using Thin-Film Magnet For Electrostatic Energy Harvester
Yoshii, S; Yamaguchi, K; Fujita, T; Kanda, K; Maenaka, K
2016-01-01
This paper proposes collision-free structure using NdFeB thin-film magnet for vibration energy harvesters. By using stripe shaped NdFeB magnet array on the Si MEMS structure, we finally obtained 3 mN of magnetic repulsive force on 8 × 8 mm 2 specimen with 40 μm air-gap. (paper)
Diagrams of the variations in the free energy of formation of metallic compounds (1960)
Darras, R.; Loriers, H.
1960-01-01
The variations in the standard free energy ΔG produced during the formation of the principal simple metallic compounds have been calculated as a function of the temperature from recently published data, and are presented in convenient diagram form. Their usefulness in metallurgy is illustrated by some possible applications. (author) [fr
Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.
Iida, Shinji; Nakamura, Haruki; Higo, Junichi
2016-06-15
We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).
Competition Experiments as a Means of Evaluating Linear Free Energy Relationships
Mullins, Richard J.; Vedernikov, Andrei; Viswanathan, Rajesh
2004-01-01
The use of competition experiments as a means of evaluating linear free energy relationship in the undergraduate teaching laboratory is reported. The use of competition experiments proved to be a reliable method for the construction of Hammett plots with good correlation providing great flexibility with regard to the compounds and reactions that…
Lee, M.W.; Meuwly, M.
2013-01-01
The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.
Experimental Determination of Third Derivative of the Gibbs Free Energy, G II
Koga, Yoshikata; Westh, Peter; Inaba, Akira
2010-01-01
We have been evaluating third derivative quantities of the Gibbs free energy, G, by graphically differentiating the second derivatives that are accessible experimentally, and demonstrated their power in elucidating the mixing schemes in aqueous solutions. Here we determine directly one of the third...
Advanced Graphene-Based Binder-Free Electrodes for High-Performance Energy Storage.
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.
Gamma-point lattice free energy estimates from O(1) force calculations
Voss, Johannes; Vegge, Tejs
2008-01-01
We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum...
Ragavan, Anpalaki J.
2006-01-01
Linear free energy relationships for trivalent cations with crystalline M 2 O 3 and, M(OH) 3 phases of lanthanides and actinides were developed from known thermodynamic properties of the aqueous trivalent cations, modifying the Sverjensky and Molling equation. The linear free energy relationship for trivalent cations is as ΔG f,MvX 0 =a MvX ΔG n,M 3+ 0 +b MvX +β MvX r M 3+ , where the coefficients a MvX , b MvX , and β MvX characterize a particular structural family of MvX, r M 3+ is the ionic radius of M 3+ cation, ΔG f,MvX 0 is the standard Gibbs free energy of formation of MvX and ΔG n,M 3+ 0 is the standard non-solvation free energy of the cation. The coefficients for the oxide family are: a MvX =0.2705, b MvX =-1984.75 (kJ/mol), and β MvX =197.24 (kJ/molnm). The coefficients for the hydroxide family are: a MvX =0.1587, b MvX =-1474.09 (kJ/mol), and β MvX =791.70 (kJ/molnm).
Free energies of stable and metastable pores in lipid membranes under tension
den Otter, Wouter K.
2009-01-01
The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to
Spontaneous symmetry breaking and self-consistent equations for the free-energy
Lovesey, S.W.
1980-03-01
A variational procedure for the free-energy is used to derive self-consistent equations that allow for spontaneous symmetry breaking. For an N-component phi 4 -model the equations are identical to those obtained by summing all loops to order 1/N. (author)
Collision-Free Structure Using Thin-Film Magnet For Electrostatic Energy Harvester
Yoshii, S.; Yamaguchi, K.; Fujita, T.; Kanda, K.; Maenaka, K.
2016-11-01
This paper proposes collision-free structure using NdFeB thin-film magnet for vibration energy harvesters. By using stripe shaped NdFeB magnet array on the Si MEMS structure, we finally obtained 3 mN of magnetic repulsive force on 8 × 8 mm2 specimen with 40 μm air-gap.
Interfacial free energy of the NaCl crystal-melt interface from capillary wave fluctuations.
Benet, Jorge; MacDowell, Luis G; Sanz, Eduardo
2015-04-07
In this work we study, by means of molecular dynamics simulations, the solid-liquid interface of NaCl under coexistence conditions. By analysing capillary waves, we obtain the stiffness for different orientations of the solid and calculate the interfacial free energy by expanding the dependency of the interfacial free energy with the solid orientation in terms of cubic harmonics. We obtain an average value for the solid-fluid interfacial free energy of 89 ± 6 mN m(-1) that is consistent with previous results based on the measure of nucleation free energy barriers [Valeriani et al., J. Chem. Phys. 122, 194501 (2005)]. We analyse the influence of the simulation setup on interfacial properties and find that facets prepared as an elongated rectangular stripe give the same results as those prepared as squares for all cases but the 111 face. For some crystal orientations, we observe at small wave-vectors a behaviour not consistent with capillary wave theory and show that this behavior does not depend on the simulation setup.
Statistical mechanical perturbation theory of solid-vapor interfacial free energy
Kalikmanov, Vitalij Iosifovitsj; Hagmeijer, Rob; Venner, Cornelis H.
2017-01-01
The solid–vapor interfacial free energy γsv plays an important role in a number of physical phenomena, such as adsorption, wetting, and adhesion. We propose a closed form expression for the orientation averaged value of this quantity using a statistical mechanical perturbation approach developed in
Statistical Mechanical Perturbation Theory of Solid−Vapor Interfacial Free Energy
Kalikmanov, V.I.; Hagmeijer, R.; Venner, C.H.
2017-01-01
The solid–vapor interfacial free energy γsv plays an important role in a number of physical phenomena, such as adsorption, wetting, and adhesion. We propose a closed form expression for the orientation averaged value of this quantity using a statistical mechanical perturbation approach developed in
Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams
Schieber, Natalie P.; Dybeck, Eric C.; Shirts, Michael R.
2018-04-01
Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of semiconductors. Predicting the most stable crystalline form at a given temperature and pressure requires determining the crystalline form with the lowest relative Gibbs free energy. Effective computational prediction of the most stable polymorph could save significant time and effort in the design of novel molecular crystalline solids or predict their behavior under new conditions. In this study, we introduce a new approach using multistate reweighting to address the problem of determining solid-solid phase diagrams and apply this approach to the phase diagram of solid benzene. For this approach, we perform sampling at a selection of temperature and pressure states in the region of interest. We use multistate reweighting methods to determine the reduced free energy differences between T and P states within a given polymorph and validate this phase diagram using several measures. The relative stability of the polymorphs at the sampled states can be successively interpolated from these points to create the phase diagram by combining these reduced free energy differences with a reference Gibbs free energy difference between polymorphs. The method also allows for straightforward estimation of uncertainties in the phase boundary. We also find that when properly implemented, multistate reweighting for phase diagram determination scales better with the size of the system than previously estimated.
Rigorous bounds on the free energy of electron-phonon models
Raedt, Hans De; Michielsen, Kristel
1997-01-01
We present a collection of rigorous upper and lower bounds to the free energy of electron-phonon models with linear electron-phonon interaction. These bounds are used to compare different variational approaches. It is shown rigorously that the ground states corresponding to the sharpest bounds do
Probing the Free Energy Landscape of the FBP28 WW Domain Using Multiple Techniques
Periole, Xavier; Allen, Lucy R.; Tamiola, Kamil; Mark, Alan E.; Paci, Emanuele
The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent.
Daily energy expenditure in free-ranging Gopher Tortoises (Gopherus polyphemus)
Jodice, PGR; Epperson, DM; Visser, GH
2006-01-01
Studies of ecological energetics in chelonians are rare. Here, we report the first measurements of daily energy expenditure (DEE) and water influx rates (WIRS) in free-ranging adult Gopher Tortoises (Gopherus polyphemus). We used the doubly labeled water (DLW) method to measure DEE in six adult
Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir
2018-04-10
We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .
Estimates of Gibbs free energies of formation of chlorinated aliphatic compounds
Dolfing, Jan; Janssen, Dick B.
1994-01-01
The Gibbs free energy of formation of chlorinated aliphatic compounds was estimated with Mavrovouniotis' group contribution method. The group contribution of chlorine was estimated from the scarce data available on chlorinated aliphatics in the literature, and found to vary somewhat according to the
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.
2014-01-01
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
Giovan, Stefan M. [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Scharein, Robert G. [Hypnagogic Software, Vancouver, British Columbia V6K 1V6 (Canada); Hanke, Andreas [Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, Texas 78520 (United States); Levene, Stephen D., E-mail: sdlevene@utdallas.edu [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Physics, University of Texas at Dallas, Richardson, Texas 75083 (United States)
2014-11-07
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Minimizing the Free Energy: A Computer Method for Teaching Chemical Equilibrium Concepts.
Heald, Emerson F.
1978-01-01
Presents a computer method for teaching chemical equilibrium concepts using material balance conditions and the minimization of the free energy. Method for the calculation of chemical equilibrium, the computer program used to solve equilibrium problems and applications of the method are also included. (HM)
Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong
2018-04-10
Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.
Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.
Liang, Huiyun; Bourdon, Allen K; Chen, Liao Y; Phelix, Clyde F; Perry, George
2018-06-11
Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K M and high V MAX , specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free energy for β-d-glucose to be -4.6 kcal/mol in agreement with the experimental value of -4.4 kcal/mol ( K M = 1.4 mM). We also compute the hydration energy of β-d-glucose, -18.0 kcal/mol vs the experimental data, -17.8 kcal/mol. In this, we establish a dynamics-based connection from GLUT3's crystal structure to its cellular thermodynamics with quantitative accuracy. We predict equal Arrhenius barriers for glucose uptake and efflux through GLUT3 to be tested in future experiments.
Longitudinal phase space manipulation in energy recovering linac-driven free-electron lasers
P. Piot
2003-03-01
Full Text Available Energy recovering an electron beam after it has participated in a free-electron laser (FEL interaction can be quite challenging because of the substantial FEL-induced energy spread and the energy antidamping that occurs during deceleration. In the Jefferson Lab infrared FEL driver accelerator, such an energy recovery scheme was implemented by properly matching the longitudinal phase space throughout the recirculation transport by employing the so-called energy compression scheme. In the present paper, after presenting a single-particle dynamics approach of the method used to energy recover the electron beam, we report on experimental validation of the method obtained by measurements of the so-called “compression efficiency” and “momentum compaction” lattice transfer maps at different locations in the recirculation transport line. We also compare these measurements with numerical tracking simulations.
Towards accurate free energy calculations in ligand protein-binding studies.
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
Mrugalla, Florian; Kast, Stefan M
2016-01-01
Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute–solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute–solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. (paper)
Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.
Awasthi, Shalini; Kapil, Venkat; Nair, Nisanth N
2016-06-15
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate.
Krivov, Sergei V
2018-06-06
Recent advances in simulation and experiment have led to dramatic increases in the quantity and complexity of produced data, which makes the development of automated analysis tools very important. A powerful approach to analyze dynamics contained in such data sets is to describe/approximate it by diffusion on a free energy landscape - free energy as a function of reaction coordinates (RC). For the description to be quantitatively accurate, RCs should be chosen in an optimal way. Recent theoretical results show that such an optimal RC exists; however, determining it for practical systems is a very difficult unsolved problem. Here we describe a solution to this problem. We describe an adaptive nonparametric approach to accurately determine the optimal RC (the committor) for an equilibrium trajectory of a realistic system. In contrast to alternative approaches, which require a functional form with many parameters to approximate an RC and thus extensive expertise with the system, the suggested approach is nonparametric and can approximate any RC with high accuracy without system specific information. To avoid overfitting for a realistically sampled system, the approach performs RC optimization in an adaptive manner by focusing optimization on less optimized spatiotemporal regions of the RC. The power of the approach is illustrated on a long equilibrium atomistic folding simulation of HP35 protein. We have determined the optimal folding RC - the committor, which was confirmed by passing a stringent committor validation test. It allowed us to determine a first quantitatively accurate protein folding free energy landscape. We have confirmed the recent theoretical results that diffusion on such a free energy profile can be used to compute exactly the equilibrium flux, the mean first passage times, and the mean transition path times between any two points on the profile. We have shown that the mean squared displacement along the optimal RC grows linear with time as for
Accuracy of free energies of hydration using CM1 and CM3 atomic charges.
Udier-Blagović, Marina; Morales De Tirado, Patricia; Pearlman, Shoshannah A; Jorgensen, William L
2004-08-01
Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water. Copyright 2004 Wiley Periodicals, Inc.
Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.
Nayar, Divya; Chakravarty, Charusita
2015-08-27
Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.
Zhihua Wang
2017-05-01
Full Text Available Crude oil is generally produced with water, and the water cut produced by oil wells is increasingly common over their lifetime, so it is inevitable to create emulsions during oil production. However, the formation of emulsions presents a costly problem in surface process particularly, both in terms of transportation energy consumption and separation efficiency. To deal with the production and operational problems which are related to crude oil emulsions, especially to ensure the separation and transportation of crude oil-water systems, it is necessary to better understand the emulsification mechanism of crude oil under different conditions from the aspects of bulk and interfacial properties. The concept of shearing energy was introduced in this study to reveal the driving force for emulsification. The relationship between shearing stress in the flow field and interfacial tension (IFT was established, and the correlation between shearing energy and interfacial Gibbs free energy was developed. The potential of the developed correlation model was validated using the experimental and field data on emulsification behavior. It was also shown how droplet deformation could be predicted from a random deformation degree and orientation angle. The results indicated that shearing energy as the energy produced by shearing stress working in the flow field is the driving force activating the emulsification behavior. The deformation degree and orientation angle of dispersed phase droplet are associated with the interfacial properties, rheological properties and the experienced turbulence degree. The correlation between shearing stress and IFT can be quantified if droplet deformation degree vs. droplet orientation angle data is available. When the water cut is close to the inversion point of waxy crude oil emulsion, the interfacial Gibbs free energy change decreased and the shearing energy increased. This feature is also presented in the special regions where
Prediction of free turbulent mixing using a turbulent kinetic energy method
Harsha, P. T.
1973-01-01
Free turbulent mixing of two-dimensional and axisymmetric one- and two-stream flows is analyzed by a relatively simple turbulent kinetic energy method. This method incorporates a linear relationship between the turbulent shear and the turbulent kinetic energy and an algebraic relationship for the length scale appearing in the turbulent kinetic energy equation. Good results are obtained for a wide variety of flows. The technique is shown to be especially applicable to flows with heat and mass transfer, for which nonunity Prandtl and Schmidt numbers may be assumed.
Free energy for protonation reaction in lithium-ion battery cathode materials
Benedek, R.; Thackeray, M. M.; van de Walle, A.
2008-01-01
Calculations are performed of free energies for proton-for-lithium-ion exchange reactions in lithium-ion battery cathode materials. First-principles calculations are employed for the solid phases and tabulated ionization potential and hydration energy data for aqueous ions. Layered structures, spinel LiMn 2 O 4 , and olivine LiFePO 4 are considered. Protonation is most favorable energetically in layered systems, such as Li 2 MnO 3 and LiCoO 2 . Less favorable are ion-exchange in spinel LiMn 2 O 4 and LiV 3 O 8 . Unfavorable is the substitution of protons for Li in olivine LiFePO 4 , because of the large distortion of the Fe and P coordination polyhedra. The reaction free energy scales roughly linearly with the volume change in the reaction
S. Alexis Paz
2018-03-01
Full Text Available In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD, adaptive-biasing forces (ABF, and on-the-fly parameterization (OTFP. We construct a simple two-dimensional potential-energy surfaces (PES that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.
Two-Dimensional Free Energy Surfaces for Electron Transfer Reactions in Solution
Shigeo Murata
2008-01-01
Full Text Available Change in intermolecular distance between electron donor (D and acceptor (A can induce intermolecular electron transfer (ET even in nonpolar solvent, where solvent orientational polarization is absent. This was shown by making simple calculations of the energies of the initial and final states of ET. In the case of polar solvent, the free energies are functions of both D-A distance and solvent orientational polarization. On the basis of 2-dimensional free energy surfaces, the relation of Marcus ET and exciplex formation is discussed. The transient effect in fluorescence quenching was measured for several D-A pairs in a nonpolar solvent. The results were analyzed by assuming a distance dependence of the ET rate that is consistent with the above model.
Low-energy electron energy losses and inelastic mean free paths in zinc, selenium, and zinc selenide
Bourke, J.D.; Chantler, C.T., E-mail: chantler@unimelb.edu.au
2014-10-15
We compute low-energy optical energy loss spectra for the elemental solids zinc and selenium, and for the binary compound zinc selenide. The optical data are transformed via a constrained partial-pole algorithm to produce momentum-dependent electron energy loss spectra and electron inelastic mean free paths. This enables a comparison between the electron scattering behaviour in a compound solid and its constituent elements. Results cannot be explained by aggregation methods or commonly used universal curves, and prove that new approaches are required. Our work demonstrates new capabilities for the determination of fundamental material properties for a range of structures previously inaccessible to established theoretical models, and at energy levels inaccessible to most experimental techniques.
Low-energy electron energy losses and inelastic mean free paths in zinc, selenium, and zinc selenide
Bourke, J.D.; Chantler, C.T.
2014-01-01
We compute low-energy optical energy loss spectra for the elemental solids zinc and selenium, and for the binary compound zinc selenide. The optical data are transformed via a constrained partial-pole algorithm to produce momentum-dependent electron energy loss spectra and electron inelastic mean free paths. This enables a comparison between the electron scattering behaviour in a compound solid and its constituent elements. Results cannot be explained by aggregation methods or commonly used universal curves, and prove that new approaches are required. Our work demonstrates new capabilities for the determination of fundamental material properties for a range of structures previously inaccessible to established theoretical models, and at energy levels inaccessible to most experimental techniques
Helmholtz resonance in a piezoelectric–hydraulic pump-based hybrid actuator
Kim, Gi-Woo; Wang, K W
2011-01-01
This paper demonstrates that a hydraulically acting Helmholtz resonator can exist in a piezoelectric–hydraulic pump (PHP) based hybrid actuator, which in turn affects the volumetric efficiency of the PHP. The simulation and experimental results illustrate the effect of Helmholtz resonance on the flow rate performance of the PHP. The study also shows how to shift the Helmholtz resonant frequency to a higher value through changing parameters such as the cylinder diameter and the effective bulk modulus of the working fluid, which will improve the volumetric efficiency and broaden the operating frequency range of the PHP actuator
Reck, Kasper; Thomsen, Erik Vilain; Hansen, Ole
2011-01-01
. The solution of the mapped Helmholtz equation is found by solving an infinite series of Poisson equations using two dimensional Fourier series. The solution is entirely based on analytical expressions and is not mesh dependent. The analytical results are compared to a numerical (finite element method) solution......The scalar wave equation, or Helmholtz equation, describes within a certain approximation the electromagnetic field distribution in a given system. In this paper we show how to solve the Helmholtz equation in complex geometries using conformal mapping and the homotopy perturbation method...
The Determinate World Kant and Helmholtz on the Physical Meaning of Geometry
Hyder, David
2009-01-01
This study examines the place of Hermann von Helmholtz´s seminal papers on geometry in his philosophy of science. The arguments of these papers are traced back to his prior work on the theory of magnitudes, as well as to Helmholtz´s early, Kantian position. The author claims that Helmholtz should be understood not as opposing Kant, but as modifying the latter´s theory of magnitudes so as to remove obstacles to their common project of constructing a complete system of natural science.
Kelvin-Helmholtz instability as a possible cause of edge localized modes
Strauss, H.R.
1992-01-01
Edge localized modes may be a Kelvin-Helmholtz instability caused by the sheared rotation of H-mode plasmas. The Kelvin-Helmholtz instability is stabilized by coupling to Alfven waves. There is a critical velocity gradient, of the order of the Alfven velocity divided by the magnetic shear length. This is verified in a numerical simulation. The critical velocity shear is consistent with experiment. A non-linear simulation shows how the Kelvin-Helmholtz mode can cause oscillations of the velocity profile. (author). Letter-to-the-editor. 13 refs, 6 figs
Free creatine available to the creatine phosphate energy shuttle in isolated rat atria
Savabi, F.
1988-01-01
To measure the actual percentage of intracellular free creatine participating in the process of energy transport, the incorporation of [1- 14 C]creatine into the free creatine and phosphocreatine (PCr) pools in spontaneously beating isolated rat atria, under various conditions, was examined. The atria were subjected to three consecutive periods, control, anoxia, and postanoxic recover, in medium containing tracers of [1- 14 C]creatine. The tissue content and specific activity of creatine and PCr were determined at the end of each period. The higher specific activity found for tissue PCr (1.87 times) than creatine, independent of the percentage of total intracellular creatine that was present as free creatine, provides evidence for the existence of two separate pools of free creatine. Analysis of the data shows that in the normal oxygenated state ∼ 9% of the total intracellular creatine is actually free to participate in the process of energy transport (shuttle pool). About 36% of the total creatine is bound to unknown intracellular components and the rest exists as PCr. The creatine that was taken up and the creatine that was released from the breakdown of PCr have much greater access to the site of phosphorylation than the rest of the intracellular creatine. A sharp increase in the specific activity of residual PCr on prolongation of anoxic time was also observed. This provides evidence for a nonhomogeneous pool of PCr, for the most recently formed (radioactive) PCr appeared to be hydrolyzed last
Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.
Will, Sebastian; Jabbari, Hosna
2016-01-01
RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free
Nordmann, R.
2011-05-01
A comprehensive review of the current situation of energy resources and consumption and of the prevailing framework like climate change is given, with a focus on Switzerland. The author, a member of the Lower House of the Swiss Parliament, presents facts and figures in a simple language, illustrated by tables and diagrams, in a well structured, easy-to-read book, with detailed indications of his data sources. Starting from the limited character of fossil energy sources, 'peak-oil' and the necessary reduction of greenhouse gas emissions, the author states that nuclear energy is not the solution. Action is absolutely needed, but which policy should be adopted? A global strategy is required that includes the stabilization of the world population as a key factor. An international agreement signed by as many states as possible should create stringent commitments. The developed countries have to demonstrate that prosperity and high life standard are compatible with an economy based on renewable energy sources. This will give to the most ambitious countries a significant advantage on new markets created by renewable energy use and energy efficiency. The author goes on by describing the current status of the technologies needed. What regards the particular case of Switzerland, this country is strongly dependent on energy import - mainly fossil - and CO 2 emissions arise mainly from the building and transportation sectors. A 50% efficiency improvement until 2030 is needed in fossil energy use. Electricity use has to become more efficient as well. Electricity generation - today about 60% renewable - shall move towards 100% renewable. The next chapters discuss clear realistic proposals on how to achieve these goals in the transportation sector ('Intelligent mobility'), the building sector ('Retrofitting the buildings to get them up-to-date') and the electrical power sector ('Entirely renewable electricity'). The title of the conclusion chapter: 'Focus again on the general
Antenna entropy in plant photosystems does not reduce the free energy for primary charge separation.
Jennings, Robert C; Zucchelli, Giuseppe
2014-12-01
We have investigated the concept of the so-called "antenna entropy" of higher plant photosystems. Several interesting points emerge: 1. In the case of a photosystemwhich harbours an excited state, the “antenna entropy” is equivalent to the configurational (mixing) entropy of a thermodynamic canonical ensemble. The energy associated with this parameter has been calculated for a hypothetical isoenergetic photosystem, photosystem I and photosystem II, and comes out in the range of 3.5 - 8% of the photon energy considering 680 nm. 2. The “antenna entropy” seems to be a rather unique thermodynamic phenomenon, in as much as it does not modify the free energy available for primary photochemistry, as has been previously suggested. 3. It is underlined that this configurational (mixing) entropy, unlike heat dispersal in a thermal system, does not involve energy dilution. This points out an important difference between thermal and electronic energy dispersal. Copyright © 2014 Elsevier B.V. All rights reserved.
Influence of an imperfect energy profile on a seeded free electron laser performance
Botao Jia
2010-06-01
Full Text Available A single-pass high-gain x-ray free electron laser (FEL calls for a high quality electron bunch. In particular, for a seeded FEL amplifier and for a harmonic generation FEL, the electron bunch initial energy profile uniformity is crucial for generating an FEL with a narrow bandwidth. After the acceleration, compression, and transportation, the electron bunch energy profile entering the undulator can acquire temporal nonuniformity. We study the influence of the electron bunch initial energy profile nonuniformity on the FEL performance. Intrinsically, for a harmonic generation FEL, the harmonic generation FEL in the final radiator starts with an electron bunch having energy modulation acquired in the previous stages, due to the FEL interaction at those FEL wavelengths and their harmonics. The influence of this electron bunch energy nonuniformity on the harmonic generation FEL in the final radiator is then studied.
Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan
2018-05-01
In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.
Energy efficient structure-free data aggregation and delivery in WSN
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.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
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.
Tomcho, Jeremy C; Tillman, Magdalena R; Znosko, Brent M
2015-09-01
Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.
Analysis of the free-energy surface of proteins from reversible folding simulations.
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.
Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan
2018-05-01
In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.
Adhesion Evaluation of Asphalt-Aggregate Interface Using Surface Free Energy Method
Jie Ji
2017-02-01
Full Text Available The influence of organic additives (Sasobit and RH and water on the adhesion of the asphalt-aggregate interface was studied according to the surface free energy theory. Two asphalt binders (SK-70 and SK-90, and two aggregate types (limestone and basalt were used in this study. The sessile drop method was employed to test surface free energy components of asphalt, organic additives and aggregates. The adhesion models of the asphalt-aggregate interface in dry and wet conditions were established, and the adhesion work was calculated subsequently. The energy ratios were built to evaluate the effect of organic additives and water on the adhesiveness of the asphalt-aggregate interface. The results indicate that the addition of organic additives can enhance the adhesion of the asphalt-aggregate interface in dry conditions, because organic additives reduced the surface free energy of asphalt. However, the organic additives have hydrophobic characteristics and are sensitive to water. As a result, the adhesiveness of the asphalt-aggregate interface of the asphalt containing organic additives in wet conditions sharply decreased due to water damage to asphalt and organic additives. Furthermore, the compatibility of asphalt, aggregate with organic additive was noted and discussed.
Analysis of Mechanical Energy Transport on Free-Falling Wedge during Water-Entry Phase
Wen-Hua Wang
2012-01-01
Full Text Available For better discussing and understanding the physical phenomena and body-fluid interaction of water-entry problem, here mechanical-energy transport (wedge, fluid, and each other of water-entry model for free falling wedge is studied by numerical method based on free surface capturing method and Cartesian cut cell mesh. In this method, incompressible Euler equations for a variable density fluid are numerically calculated by the finite volume method. Then artificial compressibility method, dual-time stepping technique, and Roe's approximate Riemann solver are applied in the numerical scheme. Furthermore, the projection method of momentum equations and exact Riemann solution are used to calculate the fluid pressure on solid boundary. On this basis, during water-entry phase of the free-falling wedge, macroscopic energy conversion of overall body-fluid system and microscopic energy transformation in fluid field are analyzed and discussed. Finally, based on test cases, many useful conclusions about mechanical energy transport for water entry problem are made and presented.
Breaking the polar-nonpolar division in solvation free energy prediction.
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
Ma, Songling; Hwang, Sungbo; Lee, Sehan; Acree, William E; No, Kyoung Tai
2018-04-23
To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described
Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.
Lev, Bogdan; Roux, Benoît; Noskov, Sergei Yu
2013-09-10
Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying
Effect of Collagen Matrix Saturation on the Surface Free Energy of Dentin using Different Agents.
de Almeida, Leopoldina de Fátima Dantas; Souza, Samilly Evangelista; Sampaio, Aline Araújo; Cavalcanti, Yuri Wanderley; da Silva, Wander José; Del Bel Cur, Altair A; Hebling, Josimeri
2015-07-01
The surface free energy of conditioned-dentin is one of the factors that interfere with monomeric infiltration of the interfibrillar spaces. Saturation of the tooth matrix with different substances may modulate this energy and, consequently, the wettability of the dentin. To evaluate the influence of different substances used to saturate conditioned-dentin on surface free energy (SFE) of this substrate. Dentin blocks (4 × 7 × 1 mm, n = 6/ group), obtained from the roots of bovine incisors, were etched using phosphoric acid for 15 seconds, rinsed and gently dried. The surfaces were treated for 60 seconds with: ultra-purified water (H20-control); ethanol (EtOH), acetone (ACT), chlorhexidine (CHX), ethylenediaminetetraacetic acid (EDTA); or sodium hypochlorite (NaOCl). The tooth surfaces were once again dried with absorbent paper and prepared for SFE evaluation using three standards: water, formamide and bromonaphthalene. Analysis of variance (ANOVA) and Dunnet's tests (a = 0.05) were applied to the data. Ethylenediaminetetraacetic acid was the only substance that caused a change to the contact angle for the standards water and formamide, while only EtOH influenced the angles formed between formamide and the dentin surface. None of the substances exerted a significant effect for bromonaphtha-lene. In comparison to the control, only EDTA and NaOCl altered both polar components of the SFE. Total SFE was increased by saturation of the collagen matrix by EDTA and reduced when NaOCl was used. Saturation of the collagen matrix by EDTA and EtOH changed the surface free energy of the dentin. In addition, the use of NaOCl negatively interfered with the properties evaluated. The increase of surface free energy and wettability of the dentin surface would allow higher penetration of the the adhesive system, which would be of importance to the clinical success of resin-dentin union.
Zhao, Lei; Gao, Jing; Liu, Qing; Zhang, Shujun; Li, Jing-Feng
2018-01-10
Lead-free dielectric ceramics with high recoverable energy density are highly desired to sustainably meet the future energy demand. AgNbO 3 -based lead-free antiferroelectric ceramics with double ferroelectric hysteresis loops have been proved to be potential candidates for energy storage applications. Enhanced energy storage performance with recoverable energy density of 3.3 J/cm 3 and high thermal stability with minimal energy density variation (<10%) over a temperature range of 20-120 °C have been achieved in W-modified AgNbO 3 ceramics. It is revealed that the W 6+ cations substitute the B-site Nb 5+ and reduce the polarizability of B-site cations, leading to the enhanced antiferroelectricity, which is confirmed by the polarization hysteresis and dielectric tunability. It is believed that the polarizability of B-site cations plays a dominant role in stabilizing the antiferroelectricity in AgNbO 3 system, in addition to the tolerance factor, which opens up a new design approach to achieve stable antiferroelectric materials.
Helmholtz Natural Modes: the universal and discrete spatial fabric of electromagnetic wavefields
El Gawhary, Omar
2017-01-01
The interaction of electromagnetic waves with matter is at the foundation of the way we perceive and explore the world around us. In fact, when a field interacts with an object, signatures on the object’s geometry and physical properties are recorded in the resulting scattered field and are transported away from the object, where they can eventually be detected and processed. An optical field can transport information through its spectral content, its polarization state, and its spatial distribution. Generally speaking, the field’s spatial structure is typically subjected to changes under free-space propagation and any information therein encoded gets reshuffled by the propagation process. We must ascribe to this fundamental reason the fact that spectroscopy was known to the ancient civilizations already, and founded as modern science in the middle of seventeenth century, while to date we do not have an established scientific of field of ‘spatial spectroscopy’ yet. In this work we tackle this issue and we show how any field, whose evolution is dictated by Helmholtz equation, contains a universal and invariant spatial structure. When expressed in the framework of this spatial fabric, the spatial information content carried by any field reveals its invariant nature. This opens the way to novel paradigms in optical digital communications, inverse scattering, materials inspection, nanometrology and quantum optics. (paper)
Förner, K.; Polifke, W.
2017-10-01
The nonlinear acoustic behavior of Helmholtz resonators is characterized by a data-based reduced-order model, which is obtained by a combination of high-resolution CFD simulation and system identification. It is shown that even in the nonlinear regime, a linear model is capable of describing the reflection behavior at a particular amplitude with quantitative accuracy. This observation motivates to choose a local-linear model structure for this study, which consists of a network of parallel linear submodels. A so-called fuzzy-neuron layer distributes the input signal over the linear submodels, depending on the root mean square of the particle velocity at the resonator surface. The resulting model structure is referred to as an local-linear neuro-fuzzy network. System identification techniques are used to estimate the free parameters of this model from training data. The training data are generated by CFD simulations of the resonator, with persistent acoustic excitation over a wide range of frequencies and sound pressure levels. The estimated nonlinear, reduced-order models show good agreement with CFD and experimental data over a wide range of amplitudes for several test cases.
Fedotov, I
2006-07-01
Full Text Available The Combined Helmholtz Integral Equation – Fourier series Formulation (CHIEFF) is based on representation of a velocity potential in terms of Fourier series and finding the Fourier coefficients of this expansion. The solution could be substantially...
Coupled Kelvin-Helmholtz and Tearing Mode Instabilities at the Mercury's Magnetopause
Ivanovski, S. L.; Milillo, A.; Kartalev, M.; Massetti, S.
2018-05-01
A MHD approach for numerical simulations of coupled Kelvin-Helmholtz and tearing mode instabilities has been applied to Mercury’s magnetopause and used to perform a physical parameters study constrained by the MESSENGER data.
National Oceanic and Atmospheric Administration, Department of Commerce — The GEOMAR Helmholtz Centre for Ocean Research Kiel made a one-time contribution to the Index to Marine and Lacustrine Geological Samples (IMLGS) database of...
Mean free paths for high energy hadron collisions in nuclear matter
Strugalski, Z.
1983-01-01
The mean free paths for various collisions of high energy pion in nuclear matter are determined experimentally using pion-xenon nucleus collision events at 3.5 GeV/c momentum. The relation between the mean free path lambdasub(i) for hadron-nucleon particle producing collisions in nuclear matter and corresponding cross section σsub(i) for particle producing collisions of this hadron with free nucleon is derived and discussed. This relation is lambdasub(i)=k/σsub(i), where lambdasub(i) is in nucleons per fm 2 and σ sub(i) - in fm 2 per nucleon, correspondingly, k=3.00+-0.26 is a coefficient accounting for the display of the nucleon inner structure in hadron-nucleus collisions
Heavy quark free energy in QCD and in gauge theories with gravity duals
Noronha, Jorge
2010-09-01
Recent lattice results in pure glue SU(3) theory at high temperatures have shown that the expectation value of the renormalized Polyakov loop approaches its asymptotic limit at high temperatures from above. We show that this implies that the “heavy quark free energy” obtained from the renormalized loop computed on the lattice does not behave like a true thermodynamic free energy. While this should be expected to occur in asymptotically free gauge theories such as QCD, we use the gauge/string duality to show that in a large class of strongly coupled gauge theories with nontrivial UV fixed points the Polyakov loop reaches its asymptotic value from above only if the dimension of the relevant operator used to deform the conformal field theory is greater than or equal to 3.
Tanuma, Shigeo; Powell, C.J.; Penn, D.R.
1990-01-01
We have proposed a general formula of electron inelastic mean free path (IMFP) to describe the calculated IMFPs over the 50-2000 eV energy range based on the Inokuti's modified Bethe formula for the inelastic scattering cross section. The IMFPs for 50-2000 eV electrons in 27 elements were calculated using Penn's algorithm. The IMFP dependence on electron energy in the range 50-200 eV varies considerably from material to material. These variations are associated with substantial differences in the electron energy-loss functions amongst the material. We also found that the modified Bethe formula by Inokuti could be fitted to the calculated IMFPs in the range 50-2000 eV within 3% relative error. (author)
Yamashita, Kazuo; Kitamura, Mitsutaka; Imai, Hideo
1976-01-01
The modified Born equation was tentatively applied to estimate the electrostatic free energies of solvation of the electron in various polar solvents. The related data of halide ions and a datum of the hydration free energy of the electron obtained by radiation chemical studies were used for the numerical calculations. (auth.)
David, Holger
2010-07-01
With saving energy in the lighting, politics, economics and private households set on compact fluorescent lamps, so called energy-saving lamps. A more economical and pollution free alternative is the increased use of daylight, which is free of charge and felt more pleasant by humans.
Monolithically integrated Helmholtz coils by 3-dimensional printing
Li, Longguang [Department of Electrical Engineering, University of Michigan–Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai 200240 (China); Abedini-Nassab, Roozbeh; Yellen, Benjamin B., E-mail: yellen@duke.edu [Department of Electrical Engineering, University of Michigan–Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai 200240 (China); Department of Mechanical Engineering and Materials Science, Duke University, P.O. Box 90300, Hudson Hall, Durham, North Carolina 27708 (United States)
2014-06-23
3D printing technology is of great interest for the monolithic fabrication of integrated systems; however, it is a challenge to introduce metallic components into 3D printed molds to enable broader device functionality. Here, we develop a technique for constructing a multi-axial Helmholtz coil by injecting a eutectic liquid metal Gallium Indium alloy (EGaIn) into helically shaped orthogonal cavities constructed in a 3D printed block. The tri-axial solenoids each carry up to 3.6 A of electrical current and produce magnetic field up to 70 G. Within the central section of the coil, the field variation is less than 1% and is in agreement with theory. The flow rates and critical pressures required to fill the 3D cavities with liquid metal also agree with theoretical predictions and provide scaling trends for filling the 3D printed parts. These monolithically integrated solenoids may find future applications in electronic cell culture platforms, atomic traps, and miniaturized chemical analysis systems based on nuclear magnetic resonance.
Monolithically integrated Helmholtz coils by 3-dimensional printing
Li, Longguang; Abedini-Nassab, Roozbeh; Yellen, Benjamin B.
2014-01-01
3D printing technology is of great interest for the monolithic fabrication of integrated systems; however, it is a challenge to introduce metallic components into 3D printed molds to enable broader device functionality. Here, we develop a technique for constructing a multi-axial Helmholtz coil by injecting a eutectic liquid metal Gallium Indium alloy (EGaIn) into helically shaped orthogonal cavities constructed in a 3D printed block. The tri-axial solenoids each carry up to 3.6 A of electrical current and produce magnetic field up to 70 G. Within the central section of the coil, the field variation is less than 1% and is in agreement with theory. The flow rates and critical pressures required to fill the 3D cavities with liquid metal also agree with theoretical predictions and provide scaling trends for filling the 3D printed parts. These monolithically integrated solenoids may find future applications in electronic cell culture platforms, atomic traps, and miniaturized chemical analysis systems based on nuclear magnetic resonance.
Reconstruction of propagating Kelvin-Helmholtz vortices at Mercury's magnetopause
Sundberg, Torbjörn; Boardsen, Scott A.; Slavin, James A.; Blomberg, Lars G.; Cumnock, Judy A.; Solomon, Sean C.; Anderson, Brian J.; Korth, Haje
2011-12-01
A series of quasi-periodic magnetopause crossings were recorded by the MESSENGER spacecraft during its third flyby of Mercury on 29 September 2009, likely caused by a train of propagating Kelvin-Helmholtz (KH) vortices. We here revisit the observations to study the internal structure of the waves. Exploiting MESSENGER's rapid traversal of the magnetopause, we show that the observations permit a reconstruction of the structure of a rolled-up KH vortex directly from the spacecraft's magnetic field measurements. The derived geometry is consistent with all large-scale fluctuations in the magnetic field data, establishes the non-linear nature of the waves, and shows their vortex-like structure. In several of the wave passages, a reduction in magnetic field strength is observed in the middle of the wave, which is characteristic of rolled-up vortices and is related to the increase in magnetic pressure required to balance the centrifugal force on the plasma in the outer regions of a vortex, previously reported in computer simulations. As the KH wave starts to roll up, the reconstructed geometry suggests that the vortices develop two gradual transition regions in the magnetic field, possibly related to the mixing of magnetosheath and magnetospheric plasma, situated at the leading edges from the perspectives of both the magnetosphere and the magnetosheath.
Kelvin-Helmholtz instability: the ``atom'' of geophysical turbulence?
Smyth, William
2017-11-01
Observations of small-scale turbulence in Earth's atmosphere and oceans have most commonly been interpreted in terms of the Kolmogorov theory of isotropic turbulence, despite the fact that the observed turbulence is significantly anisotropic due to density stratification and sheared large-scale flows. I will describe an alternative picture in which turbulence consists of distinct events that occur sporadically in space and time. The simplest model for an individual event is the ``Kelvin-Helmholtz (KH) ansatz'', in which turbulence relieves the dynamic instability of a localized shear layer. I will summarize evidence that the KH ansatz is a valid description of observed turbulence events, using microstructure measurements from the equatorial Pacific ocean as an example. While the KH ansatz has been under study for many decades and is reasonably well understood, the bigger picture is much less clear. How are the KH events distributed in space and time? How do different events interact with each other? I will describe some tentative steps toward a more thorough understanding.
Interactions between two magnetohydrodynamic Kelvin-Helmholtz instabilities
Lai, S. H.; Ip, W.-H.
2011-01-01
Kelvin-Helmholtz instability (KHI) driven by velocity shear is a generator of waves found away from the vicinity of the velocity-shear layers since the fast-mode waves radiated from the surface perturbation can propagate away from the transition layer. Thus the nonlinear evolution associated with KHI is not confined near the velocity-shear layer. To understand the physical processes in multiple velocity-shear layers, the interactions between two KHIs at a pair of tangential discontinuities are studied by two-dimensional magnetohydrodynamic simulations. It is shown that the interactions between two neighboring velocity-shear layers are dominated by the propagation of the fast-mode waves radiated from KHIs in a nonuniform medium. That is, the fast-mode Mach number of the surface waves M Fy , a key factor of the nonlinear evolution of KHI, will vary with the nonuniform background plasma velocity due to the existence of two neighboring velocity-shear layers. As long as the M Fy observed in the plasma rest frame across the neighboring velocity-shear layer is larger than one, newly formed fast-mode Mach-cone-like (MCL) plane waves generated by the fast-mode waves can be found in this region. As results of the interactions of two KHIs, reflection and distortion of the MCL plane waves generate the turbulence and increase the plasma temperature, which provide possible mechanisms of heating and accelerating local plasma between two neighboring velocity-shear layers.
Kelvin-Helmholtz instability in a bounded plasma flow
Burinskaya, T. M.
2008-01-01
Kelvin-Helmholtz instability in a three-layer plane geometry is investigated theoretically. It is shown that, in a three-layer system (in contrast to the traditionally considered case in which instability develops at the boundary between two plasma flows), instability can develop at an arbitrary ratio of the plasma flow velocity to the ion-acoustic velocity. Perturbations with wavelengths on the order of the flow thickness or longer can increase even at a zero temperature. The system can also be unstable against long-wavelength perturbations if the flow velocity at one of the boundaries is lower than the sum of the Alfven velocities in the flow and the ambient plasma. The possibility of applying the results obtained to interpret the experimental data acquired in the framework of the CLUSTER multisatellite project is discussed. It follows from these data that, in many cases, the propagation of an accelerated particle flow in the plasma-sheet boundary layer of the Earth's magnetotail is accompanied by the generation of magnetic field oscillations propagating with a velocity on the order of the local Alfven velocity.
The role of the concentration scale in the definition of transfer free energies.
Moeser, Beate; Horinek, Dominik
2015-01-01
The Gibbs free energy of transferring a solute at infinite dilution between two solvents quantifies differences in solute-solvent interactions - if the transfer takes place at constant molarity of the solute. Yet, many calculation formulae and measuring instructions that are commonly used to quantify solute-solvent interactions correspond to transfer processes in which not the molarity of the solute but its concentration measured in another concentration scale is constant. Here, we demonstrate that in this case, not only the change in solute-solvent interactions is quantified but also the entropic effect of a volume change during the transfer. Consequently, the "phenomenon" which is known as "concentration-scale dependence" of transfer free energies is simply explained by a volume-entropy effect. Our explanations are of high importance for the study of cosolvent effects on protein stability. Copyright © 2014 Elsevier B.V. All rights reserved.
Sturrock, P. A.; Antiochos, S. K.; Klinchuk, J. A.; Roumeliotis, G.
1994-01-01
It is known from computer calculations that if a force-free magnetic field configuration is stressed progressively by footpoint displacements, the configuration expands and approaches the open configuration with the same surface flux distribution and the energy of the field increases progressively. For configurations of translationalsymmetry, it has been found empirically that the energy tends asymptotically to a certain functional form. It is here shown that analysis of a simple model of the asymptotic form of force-free fields of translational symmetry leads to and therefore justifies this functional form. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.
Gibbs free energy of formation of lanthanum rhodate by quadrupole mass spectrometer
Prasad, R.; Banerjee, Aparna; Venugopal, V.
2003-01-01
The ternary oxide in the system La-Rh-O is of considerable importance because of its application in catalysis. Phase equilibria in the pseudo-binary system La 2 O 3 -Rh 2 O 3 has been investigated by Shevyakov et. al. Gibbs free energy of LaRhO 3 (s) was determined by Jacob et. al. using a solid state Galvanic cell in the temperature range 890 to 1310 K. No other thermodynamic data were available in the literature. Hence it was decided to determine Gibbs free energy of formation of LaRhO 3 (s) by an independent technique, viz. quadrupole mass spectrometer (QMS) coupled with a Knudsen effusion cell and the results are presented
Nuclear power development in Russia. Russia's energy industry preparing for the free market economy
Anon.
1993-01-01
The energy industry in Eastern Europe is preparing for the free market economy. The ambitions goal is to get fit and prepared for joining the free market economy as a competitor, and within the shortest possible time at that, struggling against the sharp wind of change that will blow, and trying to make the best of actually very unfavourable economic and political conditions. Priority has been given to privatisation of power plants and electricity networks, and to a speedy connection to the Western grids. However, all parties concerned are well aware that this task cannot be accomplished out of Russia's own resources alone. Whether the economy in Russia can be put on a stable footing and develop stable structures will depend on the development and efficient use of nuclear power, as the most important resources of Russia's energy industry are concentrated in the eastern part of the country, while 70% of electricity generation and demand is concentrated in the European part. (orig.) [de
Binder-free Si nanoparticles@carbon nanofiber fabric as energy storage material
Liu, Yuping; Huang, Kai; Fan, Yu; Zhang, Qing; Sun, Fu; Gao, Tian; Wang, Zhongzheng; Zhong, Jianxin
2013-01-01
A nonwoven nanofiber fabric with paper-like qualities composed of Si nanoparticles and carbon as binder-free anode electrode is reported. The nanofiber fabrics are prepared by convenient electrospinning technique, in which, the Si nanoparticles are uniformly confined in the carbon nanofibers. The high strength and flexibility of the nanofiber fabrics are beneficial for alleviating the structural deformation and facilitating ion transports throughout the whole composited electrodes. Due to the absence of binder, the less weight, higher energy density, and excellent electrical conductivity anodes can be attained. These traits make the composited nanofiber fabrics excellent used as a binder-free, mechanically flexible, high energy storage anode material in the next generation of rechargeable lithium ions batteries
Description of quantum coherence in thermodynamic processes requires constraints beyond free energy
Lostaglio, Matteo; Jennings, David; Rudolph, Terry
2015-01-01
Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement. PMID:25754774
Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling.
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.
Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures
Procacci, Piero
2015-01-01
In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems
QCD inequalities for the nucleon mass and the free energy of baryonic matter.
Cohen, Thomas D
2003-07-18
The positivity of the integrand of certain Euclidean space functional integrals for two flavor QCD with degenerate quark masses implies that the free energy per unit volume for QCD with a baryon chemical potential mu(B) (and zero isospin chemical potential) is greater than the free energy with an isospin chemical potential mu(I)=(2 mu(B)/N(c)) (and zero baryon chemical potential). The same result applies to QCD with any number of heavy flavors in addition to the two light flavors so long as the chemical potential is understood as applying to the light quark contributions to the baryon number. This relation implies a bound on the nucleon mass: there exists a particle X in QCD (presumably the pion) such that M(N)> or =(N(c) m(X)/2 I(X)) where m(X) is the mass of the particle and I(X) is its isospin.
Bardhan, Jaydeep P; Knepley, Matthew G
2014-10-07
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.
Bardhan, Jaydeep P.; Knepley, Matthew G.
2014-01-01
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry
Khavrutskii, Ilja V; Wallqvist, Anders
2010-11-09
This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.
Description of quantum coherence in thermodynamic processes requires constraints beyond free energy
Lostaglio, Matteo; Jennings, David; Rudolph, Terry
2015-03-01
Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement.
Bardhan, Jaydeep P.; Knepley, Matthew G.
2014-01-01
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry. PMID:25296776
Bardhan, Jaydeep P. [Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115 (United States); Knepley, Matthew G. [Computation Institute, The University of Chicago, Chicago, Illinois 60637 (United States)
2014-10-07
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.
Meisel, D
1975-07-15
Recent experimental data concerning the rate constants for electron transfer reactions of organic systems in aqueous solutions and their equilibrium constants is examined for possible correlation. The data is correlated quite well by the Marcus theory, if a reorganization parameter, lambda, of 18 kcal/mole is used. Assuming that the only contribution to lambda is the free energy of rearrangement of the water molecules, an effective radius of 5 A for the reacting entities is estimated. For the zero free energy change reaction, i.e., electron exchange between a radical ion and its parent molecule, a rate constant of about 5 X 10/sup 7/ M/sup -1/ s/sup -1/ is predicted. (auth)
Quantitative prediction of solvation free energy in octanol of organic compounds.
Delgado, Eduardo J; Jaña, Gonzalo A
2009-03-01
The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a DeltaGS0 range from about -50 to 0 kJ.mol(-1). The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ.mol(-1), just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.
Quantitative Prediction of Solvation Free Energy in Octanol of Organic Compounds
Eduardo J. Delgado
2009-03-01
Full Text Available The free energy of solvation, ΔGS0 , in octanol of organic compunds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a ΔGS0 range from about –50 to 0 kJ·mol-1. The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ·mol-1, just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.
Communication: Theoretical prediction of free-energy landscapes for complex self-assembly
Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
2015-01-14
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.
The thermodynamic properties of the upper continental crust: Exergy, Gibbs free energy and enthalpy
Valero, Alicia; Valero, Antonio; Vieillard, Philippe
2012-01-01
This paper shows a comprehensive database of the thermodynamic properties of the most abundant minerals of the upper continental crust. For those substances whose thermodynamic properties are not listed in the literature, their enthalpy and Gibbs free energy are calculated with 11 different estimation methods described in this study, with associated errors of up to 10% with respect to values published in the literature. Thanks to this procedure we have been able to make a first estimation of the enthalpy, Gibbs free energy and exergy of the bulk upper continental crust and of each of the nearly 300 most abundant minerals contained in it. Finally, the chemical exergy of the continental crust is compared to the exergy of the concentrated mineral resources. The numbers obtained indicate the huge chemical exergy wealth of the crust: 6 × 10 6 Gtoe. However, this study shows that approximately only 0.01% of that amount can be effectively used by man.
Attosecond time-energy structure of X-ray free-electron laser pulses
Hartmann, N.; Hartmann, G.; Heider, R.; Wagner, M. S.; Ilchen, M.; Buck, J.; Lindahl, A. O.; Benko, C.; Grünert, J.; Krzywinski, J.; Liu, J.; Lutman, A. A.; Marinelli, A.; Maxwell, T.; Miahnahri, A. A.; Moeller, S. P.; Planas, M.; Robinson, J.; Kazansky, A. K.; Kabachnik, N. M.; Viefhaus, J.; Feurer, T.; Kienberger, R.; Coffee, R. N.; Helml, W.
2018-04-01
The time-energy information of ultrashort X-ray free-electron laser pulses generated by the Linac Coherent Light Source is measured with attosecond resolution via angular streaking of neon 1s photoelectrons. The X-ray pulses promote electrons from the neon core level into an ionization continuum, where they are dressed with the electric field of a circularly polarized infrared laser. This induces characteristic modulations of the resulting photoelectron energy and angular distribution. From these modulations we recover the single-shot attosecond intensity structure and chirp of arbitrary X-ray pulses based on self-amplified spontaneous emission, which have eluded direct measurement so far. We characterize individual attosecond pulses, including their instantaneous frequency, and identify double pulses with well-defined delays and spectral properties, thus paving the way for X-ray pump/X-ray probe attosecond free-electron laser science.
De Beer, Stephanie B A; Glättli, Alice; Hutzler, Johannes; Vermeulen, Nico P E; Oostenbrink, Chris
2011-07-30
4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. Copyright © 2011 Wiley Periodicals, Inc.
Free radical production by high energy shock waves--comparison with ionizing irradiation.
Morgan, T R; Laudone, V P; Heston, W D; Zeitz, L; Fair, W R
1988-01-01
Fricke chemical dosimetry is used as an indirect measure of the free radical production of ionizing irradiation. We adapted the Fricke ferrous sulfate radiation dosimeter to examine the chemical effects of high energy shock waves. Significant free radical production was documented. The reaction was dose dependent, predictably increased by acoustic impedance, but curvilinear. A thousand shocks at 18 kilovolts induced the same free radical oxidation as 1100 rad cobalt-60 gamma ionizing irradiation, increasing to 2900 rad in the presence of an air-fluid zone of acoustic impedance. The biological effect of these free radicals was compared to that of cobalt-60 ionizing irradiation by measuring the affect on Chinese hamster cells by clonogenic assay. While cobalt-60 irradiation produced a marked decrease in clonogenic survivors, little effect was noted with high energy shock waves. This suggested that the chemical effects produced by shock waves were either absent or attenuated in the cells, or were inherently less toxic than those of ionizing irradiation.
Direct measurements of the Gibbs free energy of OH using a CW tunable laser
Killinger, D. K.; Wang, C. C.
1979-01-01
The paper describes an absorption measurement for determining the Gibbs free energy of OH generated in a mixture of water and oxygen vapor. These measurements afford a direct verification of the accuracy of thermochemical data of H2O at high temperatures and pressures. The results indicate that values for the heat capacity of H2O obtained through numerical computations are correct within an experimental uncertainty of 0.15 cal/mole K.
Standard Gibbs free energies for transfer of actinyl ions at the aqueous/organic solution interface
Kitatsuji, Yoshihiro; Okugaki, Tomohiko; Kasuno, Megumi; Kubota, Hiroki; Maeda, Kohji; Kimura, Takaumi; Yoshida, Zenko; Kihara, Sorin
2011-01-01
Research highlights: → Standard Gibbs free energies for ion-transfer of tri- to hexavalent actinide ions. → Determination is based on distribution method combined with ion-transfer voltammetry. → Organic solvents examined are nitrobenzene, DCE, benzonitrile, acetophenone and NPOE. → Gibbs free energies of U(VI), Np(VI) and Pu(VI) are similar to each other. → Gibbs free energies of Np(V) is very large, comparing with ordinary monovalent cations. - Abstract: Standard Gibbs free energies for transfer (ΔG tr 0 ) of actinyl ions (AnO 2 z+ ; z = 2 or 1; An: U, Np, or Pu) between an aqueous solution and an organic solution were determined based on distribution method combined with voltammetry for ion transfer at the interface of two immiscible electrolyte solutions. The organic solutions examined were nitrobenzene, 1,2-dichloroethane, benzonitrile, acetophenone, and 2-nitrophenyl octyl ether. Irrespective of the type of organic solutions, ΔG tr 0 of UO 2 2+ ,NpO 2 2+ , and PuO 2 2+ were nearly equal to each other and slightly larger than that of Mg 2+ . The ΔG tr 0 of NpO 2 + was extraordinary large compared with those of ordinary monovalent cations. The dependence of ΔG tr 0 of AnO 2 z+ on the type of organic solutions was similar to that of H + or Mg 2+ . The ΔG tr 0 of An 3+ and An 4+ were also discussed briefly.
Binder-free three-dimensional high energy density electrodes for ionic-liquid supercapacitors.
Tran, Chau; Lawrence, Daniel; Richey, Francis W; Dillard, Caitlin; Elabd, Yossef A; Kalra, Vibha
2015-09-18
We demonstrate a facile methodology to fabricate binder-free porous carbon nanofiber electrodes for room temperature ionic-liquid supercapacitors. The device provides an energy density of 80 W h kg(-1) based on the mass of two electrodes while retaining the high rate capability of supercapacitors with near-ideal CV curves at a high scan rate of 200 mV s(-1).
Free Energy Rate Density and Self-organization in Complex Systems
Georgiev, Georgi Yordanov; Gombos, Erin; Bates, Timothy; Henry, Kaitlin; Casey, Alexander; Daly, Michael
2015-01-01
One of the most important tasks in science is to understand the self-organization's arrow of time. To attempt this we utilize the connection between self-organization and non-equilibrium thermodynamics. Eric Chaisson calculated an exponential increase of Free Energy Rate Density (FERD) in Cosmic Evolution, from the Big Bang until now, paralleling the increase of system's structure. We term these studies "Devology". We connect FERD to the principle of least action for complex systems, driving ...
Surface free energy of CrN x films deposited using closed field unbalanced magnetron sputtering
Sun, C.-C.; Lee, S.-C.; Dai, S.-B.; Fu, Y.-S.; Wang, Y.-C.; Lee, Y.-H.
2006-01-01
CrN x thin films have attracted much attention for semiconductor IC packaging molding dies and forming tools due to their excellent hardness, thermal stability and non-sticking properties (low surface free energy). However, few data has been published on the surface free energy (SFE) of CrN x films at temperatures in the range 20-170 deg. C. In this study CrN x thin films with CrN, Cr(N), Cr 2 N (and mixture of these phases) were prepared using closed field unbalanced magnetron sputtering at a wide range of Cr +2 emission intensity. The contact angles of water, di-iodomethane and ethylene glycol on the coated surfaces were measured at temperatures in the range 20-170 deg. C using a Dataphysics OCA-20 contact angle analyzer. The surface free energy of the CrN x films and their components (e.g., dispersion, polar) were calculated using the Owens-Wendt geometric mean approach. The influences of CrN x film surface roughness and microstructure on the surface free energy were investigated by atomic force microscopy (AFM) and X-ray diffraction (XRD), respectively. The experimental results showed that the lowest total SFE was obtained corresponding to CrN at temperature in 20 deg. C. This is lower than that of Cr(N), Cr 2 N (and mixture of these phases). The total SFE, dispersive SFE and polar SFE of CrN x films decreased with increasing surface temperature. The film roughness has an obvious effect on the SFE and there is tendency for the SFE to increase with increasing film surface roughness
Notman, Rebecca; Anwar, Jamshed; Briels, W. J.; Noro, Massimo G.; den Otter, Wouter K.
2008-01-01
Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel pha...
On the free-energy of three-dimensional CFTs and polylogarithms
Petkou, Anastasios C.
1998-12-01
We discuss the O(N) vector model and the U(N) Gross-Neveu model with fixed total fermion number, for large-N in three dimensions. Using non-trivial polylogarithmic identities, we calculate the renormalized free-energy density of these models at their conformal points in a 'slab' geometry with one finite dimension of length L. We briefly comment on the possible implications of our results. (author)
On the free-energy of three-dimensional CFTs and polylogarithms
Petkou, Anastasios C. [Dortmund Univ. (Germany). Inst. fuer Physik; Silva Neto, Marcello B. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)
1998-12-01
We discuss the O(N) vector model and the U(N) Gross-Neveu model with fixed total fermion number, for large-N in three dimensions. Using non-trivial polylogarithmic identities, we calculate the renormalized free-energy density of these models at their conformal points in a 'slab' geometry with one finite dimension of length L. We briefly comment on the possible implications of our results. (author)
Surface energy effect on free vibration of nano-sized piezoelectric double-shell structures
Fang, Xue-Qian; Zhu, Chang-Song; Liu, Jin-Xi; Liu, Xiang-Lin
2018-01-01
Combining Goldenveizer-Novozhilov shell theory, thin plate theory and electro-elastic surface theory, the size-dependent vibration of nano-sized piezoelectric double-shell structures under simply supported boundary condition is presented, and the surface energy effect on the natural frequencies is discussed. The displacement components of the cylindrical nano-shells and annular nano-plates are expanded as the superposition of standard Fourier series based on Hamilton's principle. The total stresses with consideration of surface energy effect are derived, and the total energy function is obtained by using Rayleigh-Ritz energy method. The free vibration equation is solved, and the natural frequency is analyzed. In numerical examples, it is found that the surface elastic constant, piezoelectric constant and surface residual stress show different effects on the natural frequencies. The effect of surface piezoelectric constant is the maximum. The effect of dimensions of the double-shell under different surface material properties is also examined.
Directed influence on anaerobic energy supply systems of qualified free style wrestlers
M.G. Sybil
2015-07-01
Full Text Available Purpose: to experimentally prove effectiveness of directed influence on anaerobic energy supply systems of free style wrestlers, considering individual characteristics of their bio energetic. Material: in this article the data of laboratory bicycle stress test «Vita maxima» and results of special control testing have been presented. 40 sportsmen participated in the experiment. Results: individual characteristics of dominating type of anaerobic energy supply have been determined. Statistically confident difference between development of lactate and a-lactate anaerobic energetic components were found. By the data of bio-chemical indicators’ changes the authors observed increase of adenosine triphosphate (glycolytic or creatine-phosphate in some, weaker developed mechanisms of anaerobic re-synthesis. Ways of influence on anaerobic energy supply systems, considering individual characteristics of dominating of different components (lactate or a-lactate have been found. Conclusions: it is recommended to take in consideration individual dominating type of energy supply.
Analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field method
N.Yoshida
2007-09-01
Full Text Available An analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field (MOZ-SCF method is presented. MOZ-SCF theory is one of the theories to considering the solvent effects on the solute electronic structure in solution. [Yoshida N. et al., J. Chem. Phys., 2000, 113, 4974] Molecular geometries of water, formaldehyde, acetonitrile and acetone in water are optimized by analytical energy gradient formula. The results are compared with those from the polarizable continuum model (PCM, the reference interaction site model (RISM-SCF and the three dimensional (3D RISM-SCF.
Moraitis, Kostas; Archontis, Vasilis; Tziotziou, Konstantinos; Georgoulis, Manolis K.
We calculate the instantaneous free magnetic energy and relative magnetic helicity of solar active regions using two independent approaches: a) a non-linear force-free (NLFF) method that requires only a single photospheric vector magnetogram, and b) well known semi-analytical formulas that require the full three-dimensional (3D) magnetic field structure. The 3D field is obtained either from MHD simulations, or from observed magnetograms via respective NLFF field extrapolations. We find qualitative agreement between the two methods and, quantitatively, a discrepancy not exceeding a factor of 4. The comparison of the two methods reveals, as a byproduct, two independent tests for the quality of a given force-free field extrapolation. We find that not all extrapolations manage to achieve the force-free condition in a valid, divergence-free, magnetic configuration. This research has been co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: Thales. Investing in knowledge society through the European Social Fund.
Energy efficient rateless codes for high speed data transfer over free space optical channels
Prakash, Geetha; Kulkarni, Muralidhar; Acharya, U. S.
2015-03-01
Terrestrial Free Space Optical (FSO) links transmit information by using the atmosphere (free space) as a medium. In this paper, we have investigated the use of Luby Transform (LT) codes as a means to mitigate the effects of data corruption induced by imperfect channel which usually takes the form of lost or corrupted packets. LT codes, which are a class of Fountain codes, can be used independent of the channel rate and as many code words as required can be generated to recover all the message bits irrespective of the channel performance. Achieving error free high data rates with limited energy resources is possible with FSO systems if error correction codes with minimal overheads on the power can be used. We also employ a combination of Binary Phase Shift Keying (BPSK) with provision for modification of threshold and optimized LT codes with belief propagation for decoding. These techniques provide additional protection even under strong turbulence regimes. Automatic Repeat Request (ARQ) is another method of improving link reliability. Performance of ARQ is limited by the number of retransmissions and the corresponding time delay. We prove through theoretical computations and simulations that LT codes consume less energy per bit. We validate the feasibility of using energy efficient LT codes over ARQ for FSO links to be used in optical wireless sensor networks within the eye safety limits.
Kravchenko-Balasha, Nataly; Shin, Young Shik; Sutherland, Alex; Levine, R D; Heath, James R
2016-05-17
Controlling cell migration is important in tissue engineering and medicine. Cell motility depends on factors such as nutrient concentration gradients and soluble factor signaling. In particular, cell-cell signaling can depend on cell-cell separation distance and can influence cellular arrangements in bulk cultures. Here, we seek a physical-based approach, which identifies a potential governed by cell-cell signaling that induces a directed cell-cell motion. A single-cell barcode chip (SCBC) was used to experimentally interrogate secreted proteins in hundreds of isolated glioblastoma brain cancer cell pairs and to monitor their relative motions over time. We used these trajectories to identify a range of cell-cell separation distances where the signaling was most stable. We then used a thermodynamics-motivated analysis of secreted protein levels to characterize free-energy changes for different cell-cell distances. We show that glioblastoma cell-cell movement can be described as Brownian motion biased by cell-cell potential. To demonstrate that the free-energy potential as determined by the signaling is the driver of motion, we inhibited two proteins most involved in maintaining the free-energy gradient. Following inhibition, cell pairs showed an essentially random Brownian motion, similar to the case for untreated, isolated single cells.
Modifying Poisson equation for near-solute dielectric polarization and solvation free energy
Yang, Pei-Kun, E-mail: peikun@isu.edu.tw
2016-06-15
Highlights: • We modify the Poisson equation. • The dielectric polarization was calculated from the modified Poisson equation. • The solvation free energies of the solutes were calculated from the dielectric polarization. • The calculated solvation free energies were similar to those obtained from MD simulations. - Abstract: The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein–protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density N{sub bulk}; and relative solvent molecular density g. For a molecular solute, 4πr{sup 2}p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss’s law of Maxwell’s equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.
Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle
Isomura, Takuya; Kotani, Kiyoshi; Jimbo, Yasuhiko
2015-01-01
Blind source separation is the computation underlying the cocktail party effect––a partygoer can distinguish a particular talker’s voice from the ambient noise. Early studies indicated that the brain might use blind source separation as a signal processing strategy for sensory perception and numerous mathematical models have been proposed; however, it remains unclear how the neural networks extract particular sources from a complex mixture of inputs. We discovered that neurons in cultures of dissociated rat cortical cells could learn to represent particular sources while filtering out other signals. Specifically, the distinct classes of neurons in the culture learned to respond to the distinct sources after repeating training stimulation. Moreover, the neural network structures changed to reduce free energy, as predicted by the free-energy principle, a candidate unified theory of learning and memory, and by Jaynes’ principle of maximum entropy. This implicit learning can only be explained by some form of Hebbian plasticity. These results are the first in vitro (as opposed to in silico) demonstration of neural networks performing blind source separation, and the first formal demonstration of neuronal self-organization under the free energy principle. PMID:26690814