Ricardo Andrade

Bio: Ricardo Andrade is an academic researcher from University of São Paulo. The author has contributed to research in topics: CAN bus & Hypergraph. The author has an hindex of 8, co-authored 14 publications receiving 3814 citations. Previous affiliations of Ricardo Andrade include University of Lyon & French Institute for Research in Computer Science and Automation.

PACKMOL: a package for building initial configurations for molecular dynamics simulations.

Abstract: Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.

Analytical and Experimental Performance Evaluations of CAN-FD Bus

Abstract: Controller area network (CAN) is a widely-used bus protocol in automotive distributed embedded systems, but its limited communication bandwidth (up to 1 Mbps) and payload size (up to 8 Bytes) limit its applicability in today’s increasingly complex automotive electrical/electronic systems. CAN with flexible data rate (CAN-FD) is an improved CAN-based communication protocol, with higher communication bandwidth (up to 8 Mbps for the payload) and increased payload size (up to 64 Bytes). In this paper, we perform analytical and experimental performance comparisons of CAN-FD bus with conventional CAN bus. We consider a message set obtained by reverse-engineering a real CAN -based system, with additional high-priority interference messages for stress-testing the system with different bus loads. We also consider a networked control system based on the message set, and analyze the control system performance measured by step responses under different bus loads. Experimental results validate the performance advantages of CAN-FD over conventional CAN bus.

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Abstract: BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economically-feasible strategy for the production of novel high-value phenolic compounds isolated from berry fruits using bacterial platforms. The project aimed at covering all stages of the discovery and pre-commercialization process, including berry collection, screening and characterization of their bioactive components, identification and functional characterization of the corresponding biosynthetic pathways, and construction of Gram-positive bacterial cell factories producing phenolic compounds. Further activities included optimization of polyphenol extraction methods from bacterial cultures, scale-up of production by fermentation up to pilot scale, as well as societal and economic analyses of the processes. This review article summarizes some of the key findings obtained throughout the duration of the project.

MIP models for two-dimensional non-guillotine cutting problems with usable leftovers

Abstract: In this study we deal with the two-dimensional non-guillotine cutting problem of how to cut a set of larger rectangular objects to a set of smaller rectangular items in exactly a demanded number of pieces. We are concerned with the special case of the problem in which the non-used material of the cutting patterns (objects leftovers) may be used in the future, for example if it is large enough to fulfill future item demands. Therefore, the problem is seen as a two-dimensional non-guillotine cutting/packing problem with usable leftovers, also known in the literature as a two-dimensional residual bin-packing problem. We use multilevel mathematical programming models to represent the problem appropriately, which basically consists of cutting the ordered items using a set of objects of minimum cost, among all possible solutions of minimum cost, choosing one that maximizes the value of the usable leftovers, and, among them, selecting one that minimizes the number of usable leftovers. Because of special characteristics of these multilevel models, they can be reformulated as one-level mixed integer programming (MIP) models. Illustrative numerical examples are presented and analysed.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Abstract: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net .

CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

Abstract: CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.

Tinker 8: Software Tools for Molecular Design.

Abstract: The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field The package runs on Linux, macOS, and Windows systems In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Abstract: For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complemen...

A rechargeable zinc-air battery based on zinc peroxide chemistry

Abstract: Rechargeable alkaline zinc-air batteries promise high energy density and safety but suffer from the sluggish 4 electron (e-)/oxygen (O2) chemistry that requires participation of water and from the electrochemical irreversibility originating from parasitic reactions caused by caustic electrolytes and atmospheric carbon dioxide. Here, we report a zinc-O2/zinc peroxide (ZnO2) chemistry that proceeds through a 2e-/O2 process in nonalkaline aqueous electrolytes, which enables highly reversible redox reactions in zinc-air batteries. This ZnO2 chemistry was made possible by a water-poor and zinc ion (Zn2+)-rich inner Helmholtz layer on the air cathode caused by the hydrophobic trifluoromethanesulfonate anions. The nonalkaline zinc-air battery thus constructed not only tolerates stable operations in ambient air but also exhibits substantially better reversibility than its alkaline counterpart.