The sandfish lizard uses body undulation to swim within sand (x-ray image, left), a granular medium in which frictional forces dominate the dynamics. Numerical simulation (right) consisting of a multibody simulation of the animal coupled to a multiparticle model of the granular medium (several hundred thousand 3 mm–diameter glass spheres) allows investigation of the mechanics of swimming, including resistance forces and power consumption. In the right panel, a localized region of grains around the simulated sandfish is fluidized (brighter color indicates faster motion), while the grains only a body width away remain in a solid state. See Ding et al.
Image Credit: Yang Ding, Sarah S. Sharpe, and Andrew Masse, Georgia Institute of Technology.
Editorial
Ten Simple Rules for the Open Development of Scientific Software
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002802
Education Articles
Introduction to Translational Bioinformatics Collection
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002796
Chapter 1: Biomedical Knowledge Integration
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002826
Chapter 2: Data-Driven View of Disease Biology
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002816
Chapter 3: Small Molecules and Disease
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002805
Chapter 4: Protein Interactions and Disease
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002819
Chapter 5: Network Biology Approach to Complex Diseases
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002820
Chapter 6: Structural Variation and Medical Genomics
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002821
Chapter 7: Pharmacogenomics
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002817
Chapter 8: Biological Knowledge Assembly and Interpretation
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002858
Chapter 9: Analyses Using Disease Ontologies
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002827
Chapter 10: Mining Genome-Wide Genetic Markers
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002828
Chapter 11: Genome-Wide Association Studies
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002822
Chapter 12: Human Microbiome Analysis
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002808
Chapter 13: Mining Electronic Health Records in the Genomics Era
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002823
Chapter 14: Cancer Genome Analysis
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002824
Teaching the Fundamentals of Biological Data Integration Using Classroom Games
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002789
Review
A Comparison of Computational Models for Eukaryotic Cell Shape and Motility
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002793
Research Articles
ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002780
Localizing Genes to Cerebellar Layers by Classifying ISH Images
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002790
Sensitivity Analysis of Flux Determination in Heart by H218O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002795
Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002797
Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002798
Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures
PLOS Computational Biology: published December 13, 2012 | https://doi.org/10.1371/journal.pcbi.1002800
Modelling Hair Follicle Growth Dynamics as an Excitable Medium
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002804
SnIPRE: Selection Inference Using a Poisson Random Effects Model
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002806
Electron Transfer Interactome of Cytochrome c
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002807
Task-Dependent Changes in Cross-Level Coupling between Single Neurons and Oscillatory Activity in Multiscale Networks
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002809
Mechanics of Undulatory Swimming in a Frictional Fluid
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002810
Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli
PLOS Computational Biology: published December 13, 2012 | https://doi.org/10.1371/journal.pcbi.1002811
Quantitative Dynamics of Telomere Bouquet Formation
PLOS Computational Biology: published December 6, 2012 | https://doi.org/10.1371/journal.pcbi.1002812
Climbing Fiber Burst Size and Olivary Sub-threshold Oscillations in a Network Setting
PLOS Computational Biology: published December 13, 2012 | https://doi.org/10.1371/journal.pcbi.1002814
Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002815
The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002818
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002829
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002830
Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002832
Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002835
Soft-bound Synaptic Plasticity Increases Storage Capacity
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002836
3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002837
PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002838
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002839
The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002840
Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002841
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002844
Using Molecular Mechanics to Predict Bulk Material Properties of Fibronectin Fibers
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002845
Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner
PLOS Computational Biology: published December 20, 2012 | https://doi.org/10.1371/journal.pcbi.1002846
Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002847
Interconnected Cavernous Structure of Bacterial Fruiting Bodies
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002850
What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?
PLOS Computational Biology: published December 27, 2012 | https://doi.org/10.1371/journal.pcbi.1002851