Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the Constant Chemical Potential Molecular Dynamics (C$\mu$MD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\mu$MD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions, and to extract growth rates and free-energy barriers.Comment: 8 pages, 8 figures (Supplementary Information: 6 pages, 7 figures). Typos and labelling corrected Ver. 3: Minor comments added in Sec. 3. References 13,36,38 added. Minor text changes and typos correcte

Chemical Potential Calculations In Dense Liquids Using Metadynamics

The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.Comment: 5 pages, 2 figures, Ver 2: typos corrected, Ref. 10 year correcte

Learning Relatedness Measures for Entity Linking

Entity Linking is the task of detecting, in text documents, relevant mentions to entities of a given knowledge base. To this end, entity-linking algorithms use several signals and features extracted from the input text or from the knowl- edge base. The most important of such features is entity relatedness. Indeed, we argue that these algorithms benefit from maximizing the relatedness among the relevant enti- ties selected for annotation, since this minimizes errors in disambiguating entity-linking. The definition of an e↵ective relatedness function is thus a crucial point in any entity-linking algorithm. In this paper we address the problem of learning high-quality entity relatedness functions. First, we formalize the problem of learning entity relatedness as a learning-to-rank problem. We propose a methodology to create reference datasets on the basis of manually annotated data. Finally, we show that our machine-learned entity relatedness function performs better than other relatedness functions previously proposed, and, more importantly, improves the overall performance of dif- ferent state-of-the-art entity-linking algorithms

On Suggesting Entities as Web Search Queries

The Web of Data is growing in popularity and dimension, and named entity exploitation is gaining importance in many research fields. In this paper, we explore the use of entities that can be extracted from a query log to enhance query recommendation. In particular, we extend a state-of-the-art recommendation algorithm to take into account the semantic information associated with submitted queries. Our novel method generates highly related and diversified suggestions that we as- sess by means of a new evaluation technique. The manually annotated dataset used for performance comparisons has been made available to the research community to favor the repeatability of experiments

Chemical Potential Calculations in Non-Homogeneous Liquids

The numerical computation of chemical potential in dense, non-homogeneous fluids is a key problem in the study of confined fluids thermodynamics. To this day several methods have been proposed, however there is still need for a robust technique, capable of obtaining accurate estimates at large average densities. A widely established technique is the Widom insertion method, that computes the chemical potential by sampling the energy of insertion of a test particle. Non-homogeneity is accounted for by assigning a density dependent weight to the insertion points. However, in dense systems, the poor sampling of the insertion energy is a source of inefficiency, hampering a reliable convergence. We have recently presented a new technique for the chemical potential calculation in homogeneous fluids. This novel method enhances the sampling of the insertion energy via Well-Tempered Metadynamics, reaching accurate estimates at very large densities. In this paper we extend the technique to the case of non-homogeneous fluids. The method is successfully tested on a confined Lennard-Jones fluid. In particular we show that, thanks to the improved sampling, our technique does not suffer from a systematic error that affects the classic Widom method for non-homogeneous fluids, providing a precise and accurate result.Comment: 16 pages, 4 figures Contains a Supplementary Information fil

A scalable hardware and software control apparatus for experiments with hybrid quantum systems

Modern experiments with fundamental quantum systems - like ultracold atoms, trapped ions, single photons - are managed by a control system formed by a number of input/output electronic channels governed by a computer. In hybrid quantum systems, where two or more quantum systems are combined and made to interact, establishing an efficient control system is particularly challenging due to the higher complexity, especially when each single quantum system is characterized by a different timescale. Here we present a new control apparatus specifically designed to efficiently manage hybrid quantum systems. The apparatus is formed by a network of fast communicating Field Programmable Gate Arrays (FPGAs), the action of which is administrated by a software. Both hardware and software share the same tree-like structure, which ensures a full scalability of the control apparatus. In the hardware, a master board acts on a number of slave boards, each of which is equipped with an FPGA that locally drives analog and digital input/output channels and radiofrequency (RF) outputs up to 400 MHz. The software is designed to be a general platform for managing both commercial and home-made instruments in a user-friendly and intuitive Graphical User Interface (GUI). The architecture ensures that complex control protocols can be carried out, such as performing of concurrent commands loops by acting on different channels, the generation of multi-variable error functions and the implementation of self-optimization procedures. Although designed for managing experiments with hybrid quantum systems, in particular with atom-ion mixtures, this control apparatus can in principle be used in any experiment in atomic, molecular, and optical physics.Comment: 10 pages, 12 figure

Discovering Europeana users’ search behavior

Europeana is a strategic project funded by the European Commission with the goal of making Europe's cultural and scientific heritage accessible to the public. ASSETS is a two-year Best Practice Network co-funded by the CIP PSP Programme to improve performance, accessibility and usability of the Europeana search engine. Here we present a characterization of the Europeana logs by showing statistics on common behavioural patterns of the Europeana users

A PFEM approach to the simulation of landslide generated water-waves

A Particle Finite Element Method is here applied to the simulation of landslide-water interaction. An elastic-visco-plastic non-Newtonian, Bingham-like constitutive model has been used to describe the landslide material. Two examples are shown to show the potential of the approach