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Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics (DPD)
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems like MFsim.
Since Jdpd version 1.6.1.0 Jdpd is available in a (basic) double-precision version and a (derived) single-precision version (= JdpdSP) for all numerical calculations, where the single precision version needs about half the memory of the double precision version.
Jdpd uses the Apache Commons Math and Apache Commons RNG libraries and is published as open source under the GNU General Public License version 3. This repository comprises the Java bytecode libraries (including the Apache Commons Math and RNG libraries), the Javadoc HTML documentation and the Netbeans source code packages including Unit tests.
Jdpd has been described in the scientific literature (the final manuscript 2018 - van den Broek - Jdpd - Final Manucsript.pdf is added to the repository) and used for DPD studies (see references below).
See text file JdpdVersionHistory.txt for a version history with more detailed information.
MFsim - An open Java all-in-one rich-client simulation environment for mesoscopic simulation
MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD). The environment integrates and supports the complete preparation-simulation-evaluation triad of a mesoscopic simulation task. Productive highlights are a SPICES molecular structure editor, a PDB-to-SPICES parser for particle-based peptide/protein representations, a support of polymer definitions, a compartment editor for complex simulation box start configurations, interactive and flexible simulation box views including analytics, simulation movie generation or animated diagrams. As an open project, MFsim enables customized extensions for different fields of research.
MFsim uses several open libraries (see MFSimVersionHistory.txt for details and references below) and is published as open source under the GNU General Public License version 3 (see LICENSE).
MFsim has been described in the scientific literature and used for DPD studies.
A Robust Interface for Head Motion based Control of a Robot Arm using MARG and Visual Sensors
(2018)
Head-controlled human machine interfaces have gained popularity over the past years, especially in the restoration of the autonomy of severely disabled people, like tetraplegics. These interfaces need to be reliable and robust regarding the environmental conditions to guarantee safety of the user and enable a direct interaction between a human and a machine. This paper presents a hybrid MARG and visual sensor system for head orientation estimation which is in this case used to teleoperate a robotic arm. The system contains a Magnetic Angular Rate Gravity (MARG)-sensor and a Tobii eye tracker 4C. A MARG sensor consists of tri-axis accelerometer, gyroscope as well as a magnetometer which enable a complete measurement of orientation relative to the direction of gravity and magnetic field of the earth. The tri-axis magnetometer is sensitive to external magnetic fields which result in incorrect orientation estimation from the sensor fusion process. In this work the Tobii eye tracker 4C is used to increase head orientation estimation because it also features head tracking even though it is commonly used for eye tracking. This type of visual sensor does not suffer magnetic drift. However, it computes orientation data only, if a user is detectable. Within this work a state machine is presented which enables data fusion of the MARG and visual sensor to improve orientation estimation. The fusion of the orientation data of MARG and visual sensors enables a robust interface, which is immune against external magnetic fields. Therefore, it increases the safety of the human machine interaction.
The set of transactions that occurs on the public ledger of an Ethereum network in a specific time frame can be represented as a directed graph, with vertices representing addresses and an edge indicating the interaction between two addresses.
While there exists preliminary research on analyzing an Ethereum network by the means of graph analysis, most existing work is focused on either the public Ethereum Mainnet or on analyzing the different semantic transaction layers using static graph analysis in order to carve out the different network properties (such as interconnectivity, degrees of centrality, etc.) needed to characterize a blockchain network. By analyzing the consortium-run bloxberg Proof-of-Authority (PoA) Ethereum network, we show that we can identify suspicious and potentially malicious behaviour of network participants by employing statistical graph analysis. We thereby show that it is possible to identify the potentially malicious
exploitation of an unmetered and weakly secured blockchain network resource. In addition, we show that Temporal Network Analysis is a promising technique to identify the occurrence of anomalies in a PoA Ethereum network.