Showing papers by "Nicolae Goga published in 2013"

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

Abstract: Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches. The first makes use of improved forms for the angle potentials: the restricted bending (ReB) potential prevents torsion angles from visiting unstable or unphysical configurations and the combined bending-torsion (CBT) potential smoothly flattens the interactions when such configurations are sampled. In the second approach, dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones. For simple geometrical reasons, the unstable region is excluded from the accessible conformational space. The benefits of the new approaches are demonstrated in simulations of polyethylene glycol (PEG), polystyrene (PS), and polypeptide molecules described by the MARTINI coarse-grained force field. The new potentials are implemented in an in-house version of the Gromacs package, publicly available.

Method for measuring the heart rate through fingertip using a low-end video camera and its application in self care

Abstract: This article presents a method for monitoring the heart rate using a low-end video camera. The user places the fingertip on the camera lens and the software detects the periodic variations in light intensity caused by the pulsation of blood in the capillary tissue. The measurement technique is based on extracting beat-to-beat intervals by passing the color intensity average through a processing pipeline comprised of six stages. Our tests indicate a measurement error below 3 bpm, when compared to commonly available home care devices. We present a possible application of our method in the area of stress diagnosis and treatment. The application can be used at home to monitor personal health and enable individuals to perform enhanced self care.

StressFree--A Tool for Stress Determination and Treatment through Computer Music Generation

Abstract: This paper describes a framework for determining stress by measuring the heart rate and treating it through computer music generation. We present a practical and computationally inexpensive technique for measuring the heart rate using the low-end video cameras already present in a wide range of consumer electronics. Our method for treating stress is based on music therapy using computer generated music. Currently the heart rate monitor application and the computer music generation tool are implemented. Further work includes the analysis of heart rate variability and the integration of the framework on a smart phone.

Customized Test Data Generator for HL7v3 based Healthcare Information Systems

Abstract: Test effectiveness is a fundamental quality aspect of a test specification, which reflects its ability to demonstrate system quality levels and discover system faults. The effectiveness is tightly linked with the quality of the test data. The paper highlights specific challenges related to testing eHealth applications and emphasizes the difficulties in testing HL7v3 based applications. This paper presents a new approach on generating input test data sets: a highly customizable distance-based test data generator. The paper highlights the importance of having organized structures of test data and shows how the proposed test data generator uses adaptable distances to create clusters of test data. The generator is designed to create test data in a testing language independent format and provide means of conversion to the format used by the target testing language. A general architecture of this generator is presented, and implementation guidelines are proposed. The paper also presents the conclusions drawn from validating the generator in a real scenario.

Combining Berendsen Thermostat with Dissipative Particle Dynamics (DPD) for Polymer Simulation

Abstract: In this article we present a new thermostat - theory and simulation results - obtained by combining two thermostats Berendsen and DPD types. The new thermostat provides a predictable behavior with temperatures that do not deviate from the reference and with thermal rate constant agreement between simulations and theory. The presented work can be used for the study of polymer properties.

Trigger and Database Security

Abstract: Database Security is a growing concern evidenced by an increase in the number of reported incidencesof loss of or unauthorized exposure to sensitive data. As the amount of data collected, retained and shared electronically expands, so does the need to understand database security. Security models, developed for databases differ in many aspects because they focus on different features of the database security problem or because they make different assumptions about what constitutes a secure database. This paper explains the need for a database trigger and it role in enforcing the various database security challenges.

A Parallelization Scheme for New DPD-B Thermostats

Abstract: This paper presents the MPI parallelization of a new algorithm—DPD-B thermostat—for molecular dynamics simulations. The presented results are using Martini Coarse Grained Water System. It should be taken into account that molecular dynamics simulations are time consuming. In some cases the running time varies from days to weeks and even months. Therefore, parallelization is one solution for reducing the execution time. The paper describes the new algorithm, the main characteristics of the MPI parallelization of the new algorithm, and the simulation performances.

Questor: Medical Report Search Engine

Abstract: Quest or aims to create a novel report search engine, using ontologies and natural language processing diminishing the complexities in the report management workflow.

QUESTOR -- Automatic Searching for Reports

Abstract: Vast arrays of reporting are nowadays in use, allowing ever increasing flexibility and control over the displayed results. However, as IT developed and became available to all business domains, the number of reports used by companies started to challenge the possibility of good management. The European funded project Questor aims to create a revolutionary product that will eliminate the complexities inherent in the report management workflow. The motivation of this project is to substitute the time consuming manual search for information in reports with an automatic one. The final purpose is to make querying the report database as simple as addressing a question in natural language. This paper gives an overview over the concept of the Questor project, its software architecture and its preliminary results.