Computer Simulation

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

Evolutionary Biology / Genetics / Systematic Biology / Molecular Evolution / Phylogeny / Sequence alignment / Computer Simulation / Archaea / Bacteria / Proteins / Protein Sequence Analysis / Likelihood Functions / Sequence alignment / Computer Simulation / Archaea / Bacteria / Proteins / Protein Sequence Analysis / Likelihood Functions

Tag loss can bias Jolly-Seber capture-recapture estimates

Zoology / Computer Simulation / Common Sense / Population Size / Public Administration and Policy / Survival Rate / Capture recapture / Population Size Estimation / ENVIRONMENTAL SCIENCE AND MANAGEMENT / Survival Rate / Capture recapture / Population Size Estimation / ENVIRONMENTAL SCIENCE AND MANAGEMENT

Estimation of in vivo human brain-to-skull conductivity ratio from simultaneous extra- and intra-cranial electrical potential recordings

Engineering / Algorithms / Epilepsy / Electroencephalography / Brain Mapping / Brain / Humans / Child / Computer Simulation / Female / Clinical / Skull / Male / Human Brain / Inverse Problem / Clinical Neurophysiology / High Resolution / Electric Conductivity / Brain / Humans / Child / Computer Simulation / Female / Clinical / Skull / Male / Human Brain / Inverse Problem / Clinical Neurophysiology / High Resolution / Electric Conductivity

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

Computational Biology / Gene expression / Multidisciplinary / Next generation sequencing / Budding Yeast / Saccharomyces cerevisiae / Computer Simulation / Genome sequence / Base Sequence / Rnaseq / Condition dependence / cDNA library / Gene expression profiling / Saccharomyces cerevisiae / Computer Simulation / Genome sequence / Base Sequence / Rnaseq / Condition dependence / cDNA library / Gene expression profiling

Energy transport in peptide helices

Multidisciplinary / Macromolecular X-Ray Crystallography / Computer Simulation / Peptides / Protein Secondary Structure Prediction / Time Factors / Spectrum analysis / Time Factors / Spectrum analysis

Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties

Engineering / Macromolecular X-Ray Crystallography / Transport Properties / Computer Simulation / Physical sciences / Temperature / Deuterium / Peptides / The / CHEMICAL SCIENCES / Fourier transform infrared spectroscopy / Protein Conformation / Energy Transfer / Temperature / Deuterium / Peptides / The / CHEMICAL SCIENCES / Fourier transform infrared spectroscopy / Protein Conformation / Energy Transfer

Multifrequency vibro-acoustography

Engineering / Algorithms / Acoustics / Ultrasound / Stress field / Vibration / Acoustic Emission / Low Frequency / Humans / Computer Simulation / Scanning Acoustic Microscopy / Information Storage and Retrieval / Medical Image / Image Enhancement / Reproducibility of Results / Experimental Validation / Sensitivity and Specificity / Point Spread Function / Image Formation / Vibration / Acoustic Emission / Low Frequency / Humans / Computer Simulation / Scanning Acoustic Microscopy / Information Storage and Retrieval / Medical Image / Image Enhancement / Reproducibility of Results / Experimental Validation / Sensitivity and Specificity / Point Spread Function / Image Formation

Design of amino acid sequences to fold into Cα-model proteins

Engineering / Physical Chemistry / Protein Folding / Chemical Physics / Macromolecular X-Ray Crystallography / Humans / Computer Simulation / Lattice Beam Model / Physical sciences / Random Matrix Theory / Proteins / CHEMICAL SCIENCES / Amino Acids / Protein Secondary Structure Prediction / Amino Acid Profile / Molecular Conformation / Protein Conformation / Amino Acid Sequence / Humans / Computer Simulation / Lattice Beam Model / Physical sciences / Random Matrix Theory / Proteins / CHEMICAL SCIENCES / Amino Acids / Protein Secondary Structure Prediction / Amino Acid Profile / Molecular Conformation / Protein Conformation / Amino Acid Sequence

Combining transmural left ventricular mechanics and energetics to predict oxygen demand

Engineering / Dogs / Computer Simulation / Hemodynamics / Working Conditions / Left Ventricular Assist Device / Animals / Heart rate / Heart / Spatial Information / Mathematical Computing / Theoretical Analysis / Myocardium / Experimental Data / Oxygen Consumption / Left Ventricle / Left Ventricular Assist Device / Animals / Heart rate / Heart / Spatial Information / Mathematical Computing / Theoretical Analysis / Myocardium / Experimental Data / Oxygen Consumption / Left Ventricle

Polarization dependence of non-linear gain compression factor in semiconductor optical amplifier

Optics / Nonlinear dynamics / Semiconductors / Computer Simulation / Light / SEMICONDUCTOR OPTICAL AMPLIFIER / Polarization / Optical physics / Theoretical Models / Optics and Photonics / Amplifiers (Electronic) / Equipment Design / Theoretical Model / Equipment Failure Analysis / Electrical And Electronic Engineering / Refractometry / SEMICONDUCTOR OPTICAL AMPLIFIER / Polarization / Optical physics / Theoretical Models / Optics and Photonics / Amplifiers (Electronic) / Equipment Design / Theoretical Model / Equipment Failure Analysis / Electrical And Electronic Engineering / Refractometry

Conditional clustering of temporal expression profiles

Algorithms / Gene expression / Signal Transduction / Biological Sciences / Computer Simulation / Mathematical Sciences / Cluster Analysis / BMC Bioinformatics / Clustered Data / Clustering Method / Proteome / Time Course / Gene expression profiling / Linear Transformation / Mathematical Sciences / Cluster Analysis / BMC Bioinformatics / Clustered Data / Clustering Method / Proteome / Time Course / Gene expression profiling / Linear Transformation

3Methyladenine–DNA Glycosylase I from Escherichia coli—Computer Modeling and Supporting Experimental Evidence

Algorithms / Computer Simulation / Circular Dichroism / Escherichia coli / Biochemical / Enzyme / Protein Secondary Structure Prediction / Three Dimensional / Cysteine / Protein Conformation / Amino Acid Sequence / Biochemistry and cell biology / Enzyme / Protein Secondary Structure Prediction / Three Dimensional / Cysteine / Protein Conformation / Amino Acid Sequence / Biochemistry and cell biology

Parametric-based brain Magnetic Resonance Elastography using a Rayleigh damping material model

Algorithms / Biomedical Engineering / Brain / Humans / Computer Simulation / Viscosity / Male / Three Dimensional Imaging / Image Enhancement / Adult / Reproducibility of Results / Elastic Modulus / Sensitivity and Specificity / Viscosity / Male / Three Dimensional Imaging / Image Enhancement / Adult / Reproducibility of Results / Elastic Modulus / Sensitivity and Specificity

Multi-frequency Rayleigh damped elastography: in silico studies

Engineering / Algorithms / Finite Element Analysis / Computer Simulation / Physical sciences

Design of a switchable eliminase

Protein Folding / Catalysis / Multidisciplinary / Computer Simulation / Animals / Chickens / Calmodulin / Amino Acid Substitution Rates / Allosteric regulation / Chickens / Calmodulin / Amino Acid Substitution Rates / Allosteric regulation

Electromechanical model of excitable tissue to study reentrant cardiac arrhythmias

Finite element method / Cellular mechanotransduction / Humans / Computer Simulation / Animals / Feedback / Large Deformation Mechanics / Cardiac Arrhythmias / Finite Difference Method / Action Potentials / Body Surface Potential Mapping / Biochemistry and cell biology / Feedback / Large Deformation Mechanics / Cardiac Arrhythmias / Finite Difference Method / Action Potentials / Body Surface Potential Mapping / Biochemistry and cell biology

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