The Experts below are selected from a list of 6759 Experts worldwide ranked by ideXlab platform
Christian Holm - One of the best experts on this subject based on the ideXlab platform.
-
Espresso 4.0 – an extensible software package for simulating soft matter systems
The European Physical Journal Special Topics, 2019Co-Authors: Florian Weik, Rudolf Weeber, Kai Szuttor, Konrad Breitsprecher, Joost De Graaf, Michael Kuron, Jonas Landsgesell, Henri Menke, David Sean, Christian HolmAbstract:Espresso is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems [H.J. Limbach et al., Comput. Phys. Commun. 174, 704 (2006)]. The scope of the software has since broadened considerably: Espresso can now be used to simulate systems with length scales spanning from the molecular to the colloidal. Examples include, self-propelled particles in active matter, membranes in biological systems, and the aggregation of soot particles in process engineering. Espresso also includes solvers for hydrodynamic and electrokinetic problems, both on the continuum and on the explicit particle level. Since our last description of version 3.1 [A. Arnold et al., Meshfree methods for partial di_erential equations VI, Lect. Notes Comput. Sci. Eng. 89, 1 (2013)], the software has undergone considerable restructuring. The biggest change is the replacement of the Tcl scripting interface with a much more powerful Python interface. In addition, many new simulation methods have been implemented. In this article, we highlight the changes and improvements made to the interface and code, as well as the new simulation techniques that enable a user of Espresso 4.0 to simulate physics that is at the forefront of soft matter research.
-
Espresso - an extensible simulation package for research on soft matter systems
Computer Physics Communications, 2006Co-Authors: Hans-jörg Limbach, Axel Arnold, Bernward A. Mann, Christian HolmAbstract:Abstract We describe a new program package that is designed to perform numerical Molecular Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing Espresso was to provide a user friendly and fast simulation tool which serves at the same time as a research platform capable of rapidly incorporating the latest algorithmic developments in the field of soft matter sciences. A particular strength of Espresso is its efficient treatment of long range interactions for various geometries using sophisticated algorithms like P 3 M, MMM2D, MMM1D and ELC. It is already equipped with a broad variety of interaction potentials, thermostats, and ensemble integrators; it offers the usage of constraints, masses and rotational degrees of freedom; it allows to move between different ensembles on-the-fly. An efficient MPI parallelization allows the usage of multi-processor architectures. Strict usage of ANSI-C for the core functions and a Tcl -script driven user interface makes Espresso platform independent. This also ensures easily modifiable interfaces to communicate with other MD/MC Packages, real-time visualization and other graphic programs. We tried to maintain a clear program structure to keep Espresso extensible for future enhancements and additions. Espresso is implemented as an open source project with the goal to stimulate researchers to contribute to the package.
Axel Arnold - One of the best experts on this subject based on the ideXlab platform.
-
Espresso++: A modern multiscale simulation package for soft matter systems
Computer Physics Communications, 2013Co-Authors: Jonathan Halverson, Axel Arnold, Thomas Brandes, Olaf Lenz, Staš Bevc, Vitaliy Starchenko, Kurt Kremer, Torsten Stuehn, Dirk ReithAbstract:Abstract The redesigned Extensible Simulation Package for Research on Soft matter systems (Espresso++) is a free, open-source, parallelized, object-oriented simulation package designed to perform many-particle simulations, principally molecular dynamics and Monte Carlo, of condensed soft matter systems. In addition to the standard simulation methods found in well-established packages, Espresso++ provides the ability to perform Adaptive Resolution Scheme (AdResS) simulations which are multiscale simulations of molecular systems where the level of resolution of each molecule can change on-the-fly. With the main design objective being extensibility, the software features a highly modular C++ kernel that is coupled to a Python user interface. This makes it easy to add new algorithms, setup a simulation, perform online analysis, use complex workflows and steer a simulation. The extreme flexibility of the software allows for the study of a wide range of systems. The modular structure enables scientists to use Espresso++ as a research platform for their own methodological developments, which at the same time allows the software to grow and acquire the most modern methods. Espresso++ is targeted for a broad range of architectures and is licensed under the GNU General Public License.
-
Espresso - an extensible simulation package for research on soft matter systems
Computer Physics Communications, 2006Co-Authors: Hans-jörg Limbach, Axel Arnold, Bernward A. Mann, Christian HolmAbstract:Abstract We describe a new program package that is designed to perform numerical Molecular Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing Espresso was to provide a user friendly and fast simulation tool which serves at the same time as a research platform capable of rapidly incorporating the latest algorithmic developments in the field of soft matter sciences. A particular strength of Espresso is its efficient treatment of long range interactions for various geometries using sophisticated algorithms like P 3 M, MMM2D, MMM1D and ELC. It is already equipped with a broad variety of interaction potentials, thermostats, and ensemble integrators; it offers the usage of constraints, masses and rotational degrees of freedom; it allows to move between different ensembles on-the-fly. An efficient MPI parallelization allows the usage of multi-processor architectures. Strict usage of ANSI-C for the core functions and a Tcl -script driven user interface makes Espresso platform independent. This also ensures easily modifiable interfaces to communicate with other MD/MC Packages, real-time visualization and other graphic programs. We tried to maintain a clear program structure to keep Espresso extensible for future enhancements and additions. Espresso is implemented as an open source project with the goal to stimulate researchers to contribute to the package.
Dirk Reith - One of the best experts on this subject based on the ideXlab platform.
-
Espresso++: A modern multiscale simulation package for soft matter systems
Computer Physics Communications, 2013Co-Authors: Jonathan Halverson, Axel Arnold, Thomas Brandes, Olaf Lenz, Staš Bevc, Vitaliy Starchenko, Kurt Kremer, Torsten Stuehn, Dirk ReithAbstract:Abstract The redesigned Extensible Simulation Package for Research on Soft matter systems (Espresso++) is a free, open-source, parallelized, object-oriented simulation package designed to perform many-particle simulations, principally molecular dynamics and Monte Carlo, of condensed soft matter systems. In addition to the standard simulation methods found in well-established packages, Espresso++ provides the ability to perform Adaptive Resolution Scheme (AdResS) simulations which are multiscale simulations of molecular systems where the level of resolution of each molecule can change on-the-fly. With the main design objective being extensibility, the software features a highly modular C++ kernel that is coupled to a Python user interface. This makes it easy to add new algorithms, setup a simulation, perform online analysis, use complex workflows and steer a simulation. The extreme flexibility of the software allows for the study of a wide range of systems. The modular structure enables scientists to use Espresso++ as a research platform for their own methodological developments, which at the same time allows the software to grow and acquire the most modern methods. Espresso++ is targeted for a broad range of architectures and is licensed under the GNU General Public License.
Joaquim J. Ferreira - One of the best experts on this subject based on the ideXlab platform.
-
Espresso coffee for the treatment of somnolence in parkinson s disease results of n of 1 trials
Frontiers in Neurology, 2016Co-Authors: Tiago Mestre, Leonor Correia Guedes, Miguel Coelho, Mario M Rosa, Ana Teresa Santos, Marcio Barra, Joaquim J. Ferreira, Cristina SampaioAbstract:There is limited information available concerning the treatment of daytime somnolence associated with Parkinson’s disease (PD); the most frequently applied therapeutic strategies include decreasing the dose of dopamine agonists or adding potential wake-promoting agents. There is recent data from a placebo-controlled trial concluding on a non-significant trend in favor of caffeine. We aimed to evaluate the efficacy of Espresso-coffee in the treatment of daytime somnolence in PD. To evaluate the efficacy of Espresso-coffee in the treatment of daytime somnolence in PD, we have conducted multiple single-patient (n-of-1) clinical trials comparing regular Espresso coffee to decaffeinated coffee in PD patients presenting moderate to severe daytime somnolence defined as an Epworth Sleepiness Scale (ESS) score >9. Each single-patient (n-of-1) trial included a sequence of three crossovers (two treatment periods separated by two days of washout). Four patients were included in the studies and three completed the three pairs of treatment periods. In two of the four patients, Espresso coffee was considered beneficial. This study concludes that multiple single patient trials are feasible in PD and suggests that Espresso-coffee may have a beneficial effect on daytime somnolence in some patients. These results cannot be generalized beyond the patients included in these trials.
-
Espresso Coffee for the Treatment of Somnolence in Parkinson's Disease: Results of n-of-1 Trials.
Frontiers in neurology, 2016Co-Authors: Joaquim J. Ferreira, Tiago Mestre, Leonor Correia Guedes, Miguel Coelho, Mario M Rosa, Ana Teresa Santos, Marcio Barra, Cristina Sampaio, Olivier RascolAbstract:There is limited information available concerning the treatment of daytime somnolence associated with Parkinson's disease (PD); the most frequently applied therapeutic strategies include decreasing the dose of dopamine agonists or adding potential wake-promoting agents. There is recent data from a placebo-controlled trial concluding on a non-significant trend in favor of caffeine. We aimed to evaluate the efficacy of Espresso-coffee in the treatment of daytime somnolence in PD. To evaluate the efficacy of Espresso-coffee in the treatment of daytime somnolence in PD, we have conducted multiple single-patient (n-of-1) clinical trials comparing regular Espresso coffee to decaffeinated coffee in PD patients presenting moderate to severe daytime somnolence defined as an Epworth Sleepiness Scale score >9. Each single-patient (n-of-1) trial included a sequence of three crossovers (two treatment periods separated by two days of washout). Four patients were included in the studies and three completed the three pairs of treatment periods. In two of the four patients, Espresso coffee was considered beneficial. This study concludes that multiple single patient trials are feasible in PD and suggests that Espresso-coffee may have a beneficial effect on daytime somnolence in some patients. These results cannot be generalized beyond the patients included in these trials.
Sauro Vittori - One of the best experts on this subject based on the ideXlab platform.
-
Espresso Machine and Coffee Composition
Coffee in Health and Disease Prevention, 2014Co-Authors: Sauro Vittori, Manuela Cortese, Giovanni Caprioli, Gianni SagratiniAbstract:The aroma profile and the extraction of bioactive compounds of Espresso coffee (EC) are influenced by different EC machines working via different mechanisms and by such technical conditions as the machine extraction temperature and pressure used. The obtained data concerning the analysis by headspace solid phase micro extraction-gas chromatography-mass spectrometry of key odorants provide important information on Espresso-making technique, suggesting that 92. °C temperature and 9. bar pressure are very close to those needed to obtain the best-quality Espresso. Also, the extraction of chlorogenic acids, important antioxidant compounds, is influenced by the EC machine used. The concentrations of three chlorogenic acids (5-. O-caffeoylquinic acid, 3-. O-caffeoylquinic acid, and 3,5-di-. O-caffeoylquinic acid) in a cup of coffee ranged from 1522.5 to 2223.4. mg/kg. The concentration of total chlorogenic acids is higher in EC prepared with an Aurelia machine rather than with a Leva EC machine.
-
Importance of Espresso Coffee Machine Parameters on the Extraction of Chlorogenic Acids in a Certified Italian Espresso by Using SPE-HPLC-DAD
Journal of Food Research, 2013Co-Authors: Giovanni Caprioli, Luigi Odello, Giacomo Tomassoni, Manuela Cortese, Elisabetta Torregiani, Gianni Sagratini, Massimo Ricciutelli, Sauro VittoriAbstract:Chlorogenic acids (CGA) are a group of phenolic acid derivatives, which are commonly found in coffee at concentrations reaching 0.1-0.2%. A method based on high performance liquid chromatography-diode array detector (HPLC-DAD) is proposed for the simultaneous determination of three chlorogenic acids, i.e. 3-O-caffeoylquinic acid (3-CQA), 5-O-caffeoylquinic acid (5-CQA) and 3,5-di-O-caffeoylquinic acid (3,5-diCQA), in time portions of Espresso coffee. Two different Espresso coffee machines working with different pressure and temperature curves, and two different blends (i.e. Arabica and Robusta) were used. The method presents good linearities (correlation coefficient greater than 0.99) and recoveries (in the range 67-99%) for the 3 chlorogenic acids. The concentration of total CGAs in a cup of Certified Italian Espresso ranged from 1522.5 to 2223.4 mg kg -1 and CGA isomer contents were, in decreasing order, 5-CQA > 3-CQA > 3,5-diCQA. The concentration of total chlorogenic acids was higher in Espresso coffee (EC) prepared with Aurelia machine rather than with Leva; Arabica blend possessed higher level ot total chlorogenic acids than Robusta samples.
-
optimization of Espresso machine parameters through the analysis of coffee odorants by hs spme gc ms
Food Chemistry, 2012Co-Authors: Giovanni Caprioli, Luigi Odello, Giacomo Tomassoni, Manuela Cortese, Gianni Sagratini, Massimo Ricciutelli, Gloria Cristalli, Filippo Maggi, Veronica Sirocchi, Sauro VittoriAbstract:The aroma profile and the final quality of Espresso coffee (EC) are influenced by such technical conditions as the EC machine extraction temperature and the pressure used. The effect of these two parameters on EC quality were studied in combination by headspace solid phase micro extraction-gas chromatography-mass spectrometry (SPME-GC-MS) and sensory profile. Moreover, 10 key odorants at the best EC machine settings were examined to compare the two coffee cultivars (Arabica and Robusta) and two EC machines [Aurelia Competizione (A) and Leva Arduino (B)]. The data obtained provides important information about Espresso making technique, suggesting that the usual Espresso machine temperature and pressure settings (i.e. 92°C and 9bar) are very close to those needed to obtain the best quality Espresso. This confirms the traditional wisdom of coffee making, which judges 25ml, the typical volume of a certified Italian EC, to be ideal for very strong aroma intensity.
-
Optimization of Espresso machine parameters through the analysis of coffee odorants by HS-SPME-GC/MS.
Food chemistry, 2012Co-Authors: Giovanni Caprioli, Luigi Odello, Giacomo Tomassoni, Manuela Cortese, Gianni Sagratini, Massimo Ricciutelli, Gloria Cristalli, Filippo Maggi, Veronica Sirocchi, Sauro VittoriAbstract:The aroma profile and the final quality of Espresso coffee (EC) are influenced by such technical conditions as the EC machine extraction temperature and the pressure used. The effect of these two parameters on EC quality were studied in combination by headspace solid phase micro extraction-gas chromatography-mass spectrometry (SPME-GC-MS) and sensory profile. Moreover, 10 key odorants at the best EC machine settings were examined to compare the two coffee cultivars (Arabica and Robusta) and two EC machines [Aurelia Competizione (A) and Leva Arduino (B)]. The data obtained provides important information about Espresso making technique, suggesting that the usual Espresso machine temperature and pressure settings (i.e. 92°C and 9bar) are very close to those needed to obtain the best quality Espresso. This confirms the traditional wisdom of coffee making, which judges 25ml, the typical volume of a certified Italian EC, to be ideal for very strong aroma intensity.