The phase diagram of water at negative pressures: Virtual ices

The phase diagram of water at negative pressures as obtained from computer simulations for two models of water, TIP4P/2005 and TIP5P is presented. Several solid structures with lower densities than ice Ih, so-called virtual ices, were considered as possible candidates to occupy the negative pressure region of the phase diagram of water. In particular the empty hydrate structures sI, sII, and sH and another, recently proposed, low-density ice structure. The relative stabilities of these structures at 0 K was determined using empirical water potentials and density functional theory calculations. By performing free energy calculations and Gibbs-Duhem integration the phase diagram of TIP4P/2005 was determined at negative pressures. The empty hydrates sII and sH appear to be the stable solid phases of water at negative pressures. The phase boundary between ice Ih and sII clathrate occurs at moderate negative pressures, while at large negative pressures sH becomes the most stable phase. This behavior is in reasonable agreement with what is observed in density functional theory calculations.

Binding of Calcium and Carbonate to Polyacrylates

Polyacrylate molecules can be used to slow the growth of calcium carbonate. However, little is known about the mechanism by which the molecules impede the growth rate. A recent computational study (Bulo et al. Macromolecules 2007, 40, 3437) used metadynamics to investigate the binding of calcium to polyacrylate chains and has thrown some light on the coiling and precipitation of these polymers. We extend these simulations to examine the binding of calcium and carbonate to polyacrylate chains. We show that calcium complexed with both carbonate and polyacrylate is a very stable species. The free energies of calcium-carbonate-polyacrylate complexes, with different polymer configurations, are calculated, and differences in the free energy of the binding of carbonate are shown to be due to differences in the amount of steric hindrance about the calcium, which prevents the approach of the carbonate ion.

Measuring the Characteristic Function of the Work Distribution

We propose an interferometric setting for the ancilla-assisted measurement of the characteristic function of the work distribution following a time-dependent process experienced by a quantum system. We identify how the configuration of the effective interferometer is linked to the symmetries enjoyed by the Hamiltonian ruling the process and provide the explicit form of the operations to implement in order to accomplish our task. We finally discuss two physical settings, based on hybrid optomechanical-electromechanical devices, where the theoretical proposals discussed in our work could find an experimental demonstration.

Molecular dynamics simulation of nanoindentation of Fe3C and tetrahedral Fe4C

Study of nanomechanical response of iron carbides is important because presence of iron carbides greatly influences the performance and longevity of steel components. This work contributes to the literature by exploring nanoindentation of nanocrystalline Fe3C and tetrahedral-Fe4C using molecular dynamics simulation. The chemical interactions of iron and carbon were described through an analytical bond order inter-atomic potential (ABOP) energy function. The indentations were performed at an indentation speed of 50 m/sec and a repeat trial was performed at 5 m/sec. Load-displacement (P-h) curve for both these carbides showed residual indentation depth and maximum indentation depth (hf/hmax) ratio to be higher than 0.7 i.e. a circumstance where Oliver and Pharr method was not appropriate to be applied to evaluate the material properties. Alternate evaluation revealed Fe3C to be much harder than Fe4C. Gibbs free energy of formation and radial distribution function, coupled with state of the average local temperature and von Mises stresses indicate the formation of a new phase of iron-carbide. Formation of this newer phase was found to be due to deviatoric strain rather than the high temperature induced in the substrate during nanoindentation

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Detecting the work statistics through Ramsey-like interferometry

Out-of-equilibrium statistical mechanics is attracting considerable interest due to the recent advances in the control and manipulations of systems at the quantum level. Recently, an interferometric scheme for the detection of the characteristic function of the work distribution following a time-dependent process has been proposed [L. Mazzola et al., Phys. Rev. Lett. 110 (2013) 230602]. There, it was demonstrated that the work statistics of a quantum system undergoing a process can be reconstructed by effectively mapping the characteristic function of work on the state of an ancillary qubit. Here, we expand that work in two important directions. We first apply the protocol to an interesting specific physical example consisting of a superconducting qubit dispersively coupled to the field of a microwave resonator, thus enlarging the class of situations for which our scheme would be key in the task highlighted above. We then account for the interaction of the system with an additional one (which might embody an environment), and generalize the protocol accordingly.

Low pressure methane solubility in lithium-ion batteries based solvents and electrolytes as a function of temperature. Measurement and prediction

The methane solubility in five pure electrolyte solvents and one binary solvent mixture for lithium ion batteries – such as ethylene carbonate (EC), propylene carbonate (PC), dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), diethyl carbonate (DEC) and the (50:50 wt%) mixture of EC:DMC was studied experimentally at pressures close to atmospheric and as a function of temperature between (280 and 343) K by using an isochoric saturation technique. The effect of the selected anions of a lithium salt LiX (X = hexafluorophosphate,

Levoglucosan formation mechanisms during cellulose pyrolysis

Levoglucosan is one important primary product during cellulose pyrolysis either as an intermediate or as a product. Three available mechanisms for levoglucosan formation have been studied theoretically in this paper, which are free-radical mechanism; glucose intermediate mechanism; and levoglucosan chain-end mechanism. All the elementary reactions included in the pathway of every mechanism were investigated; thermal properties including activation energy, Gibbs free energy, and enthalpy for every pathway were also calculated. It was concluded that free-radical mechanism has the highest energy barrier during the three levoglucosan formation mechanisms, glucose intermediate mechanism has lower energy barrier than free-radical mechanism, and levoglucosan chain-end mechanism is the most reasonable pathway because of the lowest energy barrier. By comparing with the activation energy obtained from the experimental results, it was also concluded that levoglucosan chain-end mechanism fits better with the experimental data for the formation of levoglucosan. © 2013 Elsevier B.V. All rights reserved.

Nonequilibrium Quantum Landauer Principle

Using the operational framework of completely positive, trace preserving operations and thermodynamic fluctuation relations, we derive a lower bound for the heat exchange in a Landauer erasure process on a quantum system. Our bound comes from a nonphenomenological derivation of the Landauer principle which holds for generic nonequilibrium dynamics. Furthermore, the bound depends on the nonunitality of dynamics, giving it a physical significance that differs from other derivations. We apply our framework to the model of a spin-1/2 system coupled to an interacting spin chain at finite temperature.

Activity and coke formation of nickel and nickel carbide in dry reforming: A deactivation scheme from density functional theory

Dry reforming is a promising reaction to utilise the greenhouse gases CO2 and CH4. Nickel-based catalysts are the most popular catalysts for the reaction, and the coke formation on the catalysts is the main obstacle to the commercialisation of dry reforming. In this study, the whole reaction network of dry reformation on both flat and stepped nickel catalysts (Ni(111) and Ni(211)) as well as nickel carbide (flat: Ni3C(001); stepped: Ni3C(111)) is investigated using density functional theory calculations. The overall reaction energy profiles in the free energy landscape are obtained, and kinetic analyses are utilised to evaluate the activity of the four surfaces. By careful examination of our results, we find the following regarding the activity: (i) flat surfaces are more active than stepped surfaces for the dry reforming and (ii) metallic nickel catalysts are more active than those of nickel carbide, and therefore, the phase transformation from nickel to nickel carbide will reduce the activity. With respect to the coke formation, the following is found: (i) the coke formation probability can be measured by the rate ratio of CH oxidation pathway to C oxidation pathway (r(CH)/r(C)) and the barrier of CO dissociation, (ii) on Ni(111), the coke is unlikely to form, and (iii) the coke formations on the stepped surfaces of both nickel and nickel carbide can readily occur. A deactivation scheme, using which experimental results can be rationalised, is proposed. 

Density functional theory study on the activation of molecular oxygen on a stepped gold surface in an aqueous environment: a new approach for simulating reactions in solution

The activation of oxygen molecules is an important issue in the gold-catalyzed partial oxidation of alcohols in aqueous solution. The complexity of the solution arising from a large number of solvent molecules makes it difficult to study the reaction in the system. In this work, O-2 activation on an Au catalyst is investigated using an effective approach to estimate the reaction barriers in the presence of solvent. Our calculations show that O-2 can be activated, undergoing OOH* in the presence of water molecules. The OOH* can readily be formed on Au(211) via four possible pathways with almost equivalent free energy barriers at the aqueous-solid interface: the direct or indirect activation of O-2 by surface hydrogen or the hydrolysis of O-2 following a Langmuir-Hinshelwood mechanism or an Eley-Rideal mechanism. Among them, the Eley-Rideal mechanism may be slightly more favorable due to the restriction of the low coverage of surface H on Au(211) in the other mechanisms. The results shed light on the importance of water molecules on the activation of oxygen in gold-catalyzed systems. Solvent is found to facilitate the oxygen activation process mainly by offering extra electrons and stabilizing the transition states. A correlation between the energy barrier and the negative charge of the reaction center is found. The activation barrier is substantially reduced by the aqueous environment, in which the first solvation shell plays the most important role in the barrier reduction. Our approach may be useful for estimating the reaction barriers in aqueous systems.

Probing The effects of Experimental Conditions on the Character of Drug-Polymer Phase Diagrams Constructed Using Flory-Huggins Theory

Purpose: Amorphous drug-polymer solid dispersions have been found to result in improved drug dissolution rates when compared to their crystalline counterparts. However, when the drug exists in the amorphous form it will possess a higher Gibb’s free energy than its associated crystalline state and can recrystallize. Drug-polymer phase diagrams constructed through the application of the Flory Huggins (F-H) theory contain a wealth of information regarding thermodynamic and kinetic stability of the amorphous drug-polymer system. This study was aimed to evaluate the effects of various experimental conditions on the solubility and miscibility detections of drug-polymer binary system. Methods: Felodipine (FD)-Polyvinylpyrrolidone (PVP) K15 (PVPK15) and FD-Polyvinylpyrrolidone/vinyl acetate (PVP/VA64) were the selected systems for this research. Physical mixtures with different drug loadings were mixed and ball milled. These samples were then processed using Differential Scanning Calorimetry (DSC) and measurements of melting point (Tend) and glass transition (Tg) were detected using heating rates of 0.5, 1.0 and 5.0°C/min. Results: The melting point depression data was then used to calculate the F-H interaction parameter (χ) and extrapolated to lower temperatures to complete the liquid–solid transition curves. The theoretical binodal and spinodal curves were also constructed which were used to identify regions within the phase diagram. The effects of polymer selection, DSC heating rate, time above parent polymer Tg and polymer molecular weight were investigated by identifying amorphous drug miscibility limits at pharmaceutically relevant temperatures. Conclusion: The potential implications of these findings when applied to a non-ambient processing method such as Hot Melt Extrusion (HME) are also discussed.

Modelação molecular de associações entre aniões e receptores sintéticos

A aplicação de simulações de mecânica e dinâmica molecular ao estudo de sistemas supramoleculares tem adquirido, ao longo dos últimos anos, enorme relevância. A sua utilização não só tem levado a uma melhor compreensão dos mecanismos de formação desses mesmos sistemas, como também tem fornecido um meio para o desenvolvimento de novas arquitecturas supramoleculares. Nesta tese são descritos os trabalhos de mecânica e dinâmica molecular desenvolvidos no âmbito do estudo de associações supramoleculares entre aniões e receptores sintéticos do tipo [2]catenano, [2]rotaxano e pseudorotaxano. São ainda estudados complexos supramoleculares envolvendo receptores heteroditópicos do tipo calix[4]diquinona e pares iónicos formados por aniões halogeneto e catiões alcalinos e amónio. Os estudos aqui apresentados assentam essencialmente em duas vertentes: no estudo das propriedades dinâmicas em solução dos vários complexos supramoleculares considerados e no cálculo das energias livres de Gibbs de associação relativas dos vários iões aos receptores sintéticos. As metodologias utilizadas passaram por dinâmica molecular convencional e REMD (Replica Exchange Molecular Dynamics), para o estudo das propriedades em solução, e por cálculos de integração termodinâmica e MMPBSA (Molecular Mechanics – Poisson Boltzmann Surface Area), para a computação das energias livres de associação relativas. Os resultados obtidos, além de terem permitido uma visão mais detalhada dos mecanismos envolvidos no reconhecimento e associação dos vários receptores aos aniões e pares iónicos abordados, encontram-se, globalmente, de acordo com os análogos determinados experimentalmente, validando assim as metodologias empregadas. Em jeito de conclusão, investigou-se ainda a capacidade de um dos receptores heteroditópicos estudados para assistir favoravelmente na migração do par iónico KCl através da interface água-clorofórmio. Para tal, foram utilizadas simulações SMD (Steered Molecular Dynamics) para a computação do perfil de energia livre de Gibbs associada à migração do par iónico através da interface.

Monte Carlo studies of phase transitions and adsorption : application to n-6 Lennard-Jones, C60 and zeolite systems

The solid-fluid transition properties of the n - 6 Lennard-Jones system are studied by means of extensive free energy calculations. Different values of the parameter n which regulates the steepness of the short-range repulsive interaction are investigated. Furthermore, the free energies of the n < 12 systems are calculated using the n = 12 system as a reference. The method relies on a generalization of the multiple histogram method that combines independent canonical ensemble simulations performed with different Hamiltonians and computes the free energy difference between them. The phase behavior of the fullerene C60 solid is studied by performing NPT simulations using atomistic models which treat each carbon in the molecule as a separate interaction site with additional bond charges. In particular, the transition from an orientationally frozen phase at low temperatures to one where the molecules are freely rotating at higher temperatures is studied as a function of applied pressure. The adsorption of molecular hydrogen in the zeolite NaA is investigated by means of grand-canonical Monte Carlo, in a wide range of temperatures and imposed gas pressures, and results are compared with available experimental data. A potential model is used that comprises three main interactions: van der Waals, Coulomb and induced polarization by the permanent electric field in the zeolite.

An analysis of decoupling procedures in generating thermal Green's functions of O([lambda]â ´) by the Zubarev equation of motion method

The Zubarev equation of motion method has been applied to an anharmonic crystal of O( ,,4). All possible decoupling schemes have been interpreted in order to determine finite temperature expressions for the one phonon Green's function (and self energy) to 0()\4) for a crystal in which every atom is on a site of inversion symmetry. In order to provide a check of these results, the Helmholtz free energy expressions derived from the self energy expressions, have been shown to agree in the high temperature limit with the results obtained from the diagrammatic method. Expressions for the correlation functions that are related to the mean square displacement have been derived to 0(1\4) in the high temperature limit.