Compression of Vector Field Changing in Time

One of the problems connected with a real-time protein-ligand docking simulation is the need to store series of precomputed electrostatic force fields of a molecule changing in time. A single frame of the force field is a 3D array of floating point vectors and it constitutes approximately 180 MB of data. Therefore requirements on storage grow rapidly if several hundreds of such frames need to be stored. We propose a lossy compression method of such force field, based on audio and video coding, and we evaluate its properties and performance

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions

Haptic Rendering of Molecular Conformations

Current computational simulation are capable of producing enromous amounts of data. Complete understanding of their features presents a challenge even if very sophisticated visualization techniques are deployed. Computational analysis of conformational behaviour of biologically active compounds represents such simulation. We investigate methods how haptic rendering may contribute to better and faster understanding of the simulation results. This paper presents current progress in our research. I. Molecular Flexibility and Conformational Behaviour Many molecules exhibit an important chemical property --- flexibility. Biological activity of large molecules is directly related to their flexibility. The flexibility can be described in terms of conformational behaviour of the molecule. Undergoing the behaviour, the molecule changes its shape (config- uration) only, no chemical bonds are either created or broken, as well as the absolute configuration on atoms (or other chiral centres) does not change. Roughly speaking, internal potential energy of the molecule is a function of the configuration, therefore, in general, not all the configurations are favoured equally. By conformations we mean local potential energy minima, i. e. the configurations that are more stable than the others. Then the conformational behaviour is the process of traversing among conformations via transition states

An Algorithm on Interpolating between Two Shapes of a Molecule

Conformational behaviour analysis produces a sequence of shapes of a molecule which are only the key points on the entire path. They differ from one another significantly and an interpolation is necessary to achieve a smooth visualization. However, standard interpolation techniques cannot be used. We introduce a hypothesis on the nature of the shape changes and derive an interpolation algorithm. Conditions required for proper function as well as some ideas how to overcome the algorithm's drawbacks are presented. 1 Chemical background A simulation of conformational behaviour is an important part of computational chemistry. Unlike reactions this behaviour of a molecule involves changes in the shape of the molecule (called geometry here) only, bonds are neither created nor destroyed (the topology does not change). Among all such possible geometries of a single molecule there are two categories of special interest . Conformers (or conformations) are the stable ones in terms of potential ..

Studying Conformational Behaviour with Phantom Device

In this paper we present a current state of research in the field of examining scientific (especially chemical) data via haptic devices. The first section shows our technical solution---PHANToM driver in RT Linux, the second one is a case study describing our application in development. 1 PHANToM in RT Linux 1.1 Motivation Currently Sensable supports only two platforms with its PHANToM device---Windows NT and SGI IRIX. However, in the time we started our experiments none of those OS's provided realtime extension. For direct interaction with the PHANToM device we required true multitasking support, networking and preferably hard real-time OS. We decided to use RT-linux [1] which is very stable in its release 1.1. This version is designed for the 2.0.36 linux kernel. A version for 2.2 kernel is under development, however, in this moment it is not stable enough to be deployed in an application. 1.2 Driver development Sensable doesn't support other platforms and doesn't provide any..

The First Provenance Challenge

The first Provenance Challenge was a community activity aiming at understanding the expressiveness of provenance representations and capabilities of provenance systems. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Seventeen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions