351981
Real-time Animation Technique for Flexible and Thin Objects
In this paper, we propose an e cient technique for the animation of exible thin objects. Massspring model was employed to represent the exible objects. Many techniques have used the mass-spring model to generate plausible animation of soft objects. The easiest approach to animation with mass-spring model is explicit Euler method, but the explicit Euler method has serious disadvantage that it su ers from `instability problem'. The implicit integration method is a possible solution to overcome the instability problem. However, the most critical aw of the implicit method is that it involves a large linear system. This paper presents a fast animation technique for mass-spring model with approximated implicit method. The proposed technique stably updates the state of n mass-points in O(n) time when the number of total springs are O(n). We also consider the interaction of the exible object and air in order to generate plausible results.
10262654
COMPAM : visualization of combining pairwise alignments for multiple genomes
UNLABELLED
COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.


AVAILABILITY
http://bio.informatics.indiana.edu/projects/compam/
6230675
ARCS: an aggregated related column scoring scheme for aligned sequences
MOTIVATION
Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.


RESULTS
This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.


AVAILABILITY
The source code is available on http://bio.informatics.indiana.edu/projects/arcs and http://goldengate.case.edu/projects/arcs
16784503
PhyloDraw: a phylogenetic tree drawing system
UNLABELLED
PhyloDraw is a unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript.


AVAILABILITY
http://pearl.cs.pusan.ac.kr/phylodraw/


CONTACT
jhchoi@pearl.cs.pusan.ac.kr
16977036
Element-Free Elastic Models for Volume Fitting and Capture
We present a new method of fitting an element-free volumetric model to a sequence of deforming surfaces of a moving object. Given a sequence of visual hulls, we iteratively fit an element-free elastic model to the visual hull in order to extract the optimal pose of the captured volume. The fitting of the volumetric model is acheived by minimizing a combination of elastic potential energy, a surface distance measure, and a self-intersection penalty for each frame. A unique aspect of our work is that the model is mesh free - since the model is represented as a point cloud, it is easy to construct, manipulate and update the model as needed. Additionally, linear elasicity with rotation compensation makes it possible to handle local deformations and large rotations of body parts much more efficiently than other volume fitting approaches. Our experimental results for volume fitting and capture in a multi-view camera setting demonstrate the robustness of element-free elastic models against noise and self-occlusions.
10945598
An efficient merging algorithm for recovery and garbage collection in incremental checkpointing
13403233
Auditable Privacy: On Tamper-Evident Mix Networks
We introduce the notion of tamper-evidence for mix networks in order to defend against attacks aimed at covertly leaking secret information held by corrupted mix servers. This is achieved by letting observers (which need not be trusted) verify the absence of covert channels by means of techniques we introduce herein. Our tamper-evident mix network is a type of re-encryption mixnet in which a server proves that the permutation and re-encryption factors that it uses are correctly derived from a random seed to which the server is committed.
926635
Escape analysis for Java
This paper presents a simple and efficient data flow algorithm for escape analysis of objects in Java programs to determine (i) if an object can be allocated on the stack; (ii) if an object is accessed only by a single thread during its lifetime, so that synchronization operations on that object can be removed. We introduce a new program abstraction for escape analysis, the connection graph, that is used to establish reachability relationships between objects and object references. We show that the connection graph can be summarized for each method such that the same summary information may be used effectively in different calling contexts. We present an interprocedural algorithm that uses the above property to efficiently compute the connection graph and identify the non-escaping objects for methods and threads. The experimental results, from a prototype implementation of our framework in the IBM High Performance Compiler for Java, are very promising. The percentage of objects that may be allocated on the stack exceeds 70% of all dynamically created objects in three out of the ten benchmarks (with a median of 19%), 11% to 92% of all lock operations are eliminated in those ten programs (with a median of 51%), and the overall execution time reduction ranges from 2% to 23% (with a median of 7%) on a 333 MHz PowerPC workstation with 128 MB memory.
5394476
Cross-Layer Analysis of Rate Adaptation, DCF and TCP in Multi-Rate WLANs
Wireless Internet access is facilitated by IEEE 802.11 WLANs that, in addition to realizing a specific form of CSMA/CA-distributed coordination function (DCF)- implement a range of performance enhancement features such as multi-rate adaptation that induce cross-layer protocol coupling. Recent works in empirical WLAN performance evaluation have shown that cross-layer interactions can be subtle, sometimes leading to unexpected outcomes. Two such instances are: significant throughput degradation (a bell-shaped throughput curve) resulting from automatic rate fallback (ARF) having difficulty distinguishing collision from channel noise, and scalable TCP performance over DCF that is able to curtail effective multiple access contention in the presence of many contending stations. The latter also mitigates the negative performance effect of ARF. In this paper, we present station-centric Markov chain models of WLAN cross-layer performance aimed at capturing complex interactions between ARF, DCF, and TCP. Our performance analyses may be viewed as multi-protocol extensions of Bianchi's IEEE 802.11 model that, despite significantly increased complexity, lead to tractable and accurate performance predictions due to modular coupling. Our results complement empirical and simulation-based findings, demonstrating the versatility and efficacy of station-centric Markov chain analysis for capturing cross-layer WLAN dynamics.