771 Works

Campylobacter jejuni

Atlas of Bacterial and Archaeal Cell Structure

Helicobacter pylori

Atlas of Bacterial and Archaeal Cell Structure

Halomicrobium mukohataei

Atlas of Bacterial and Archaeal Cell Structure

Ultraviolet Radiation of Hypervelocity Stagnation Flows and Shock/Boundary-Layer Interactions

Nelson Javier Yanes
Shock/boundary-layer interactions can induce flow distortion, create flow separation with loss of control authority, and result in high thermal loads. Correct prediction of the flow structure and heating loads is vital for vehicle survival. However, a recent NATO workshop revealed severe underprediction of thermal loads and discrepancies in the location of separation by simulations of high enthalpy air flows. Due to the coupling between thermochemistry and fluid mechanics, a substantial effort has been placed on...

sbmlteam/libCombine: Initial Release

Initial release of libCombine, a C++ API library supporting the COMBINE Archive. This release is made in order to elicit feedback on how to improve the API. This library supports: - C++ - .NET - Java - Python Examples are available online: - [Examples](https://github.com/sbmlteam/libCombine/tree/master/examples) Rudimentary documentation is online here: - [CombineArchive](https://sbmlteam.github.io/libCombine/html/class_combine_archive.html) For more information and instructions for building the library see README.md.

Mycoplasma genitalium

Atlas of Bacterial and Archaeal Cell Structure

Listeria monocytogenes

Atlas of Bacterial and Archaeal Cell Structure

Borrelia burgdorferi

Atlas of Bacterial and Archaeal Cell Structure

Prosthecobacter debontii

Atlas of Bacterial and Archaeal Cell Structure

Visualizing Small Proteins with the cryoEM Platform and The Structure of the Vibrio cholerae Type IV Competence Pilus Secretin PilQ

Sara Jean Weaver
Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs,...

CITE-seq protein and mRNA counts

Gennady Gorin, Valentine Svensson & Lior Pachter
Protein counts were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866. LOOM was generated from FASTQ. cellranger processing: cellranger count --id=(desired bam directory) --transcriptome=(transcriptome directory) --fastqs=(fastq directory) --localcores=40 --localmem=100 --chemistry=SC3Pv2 velocyto processing: velocyto run10x --samtools-threads 60 --samtools-memory 5000 (desired bam directory) (transcriptome directory)/genes/genes.gtf

Thermal Conduction in Amorphous Materials and the Role of Collective Excitations

Jaeyun Moon
The atomic vibrations and thermal properties of amorphous dielectric solids are of fundamental and practical interest. For applications, amorphous solids are widely used as thermal insulators in thermopile and other detectors where low thermal conductivity directly sets the sensitivity of the detector. Amorphous solids are of fundamental interest themselves because the lack of atomic periodicity complicates theoretical development. As a result, the lower limits of thermal conductivity in solids as well as the nature of...

Subspace Subcodes of Reed-Solomon Codes

Masayuki Hattori
In this paper we introduce a new class of non-linear cyclic error-correcting codes, which we call subspace subcodes of Reed-Solomon (SSRS) codes. An SSRS code is a subset of a parent Reed-Solomon (RS) code consisting of codewords whose components all lie in a fixed v-dimensional vector subspace S of GF(2ᵐ). Starting from a (n, k₀, d₀) RS code over GF(2ᵐ), with any positive integer 0 ≤ v ≤ m, there is an SSRS code of...

Data for \"Assessment of InSight Landing Site Predictions\"

Matthew Golombek
This file describes data related to Golombek et al. 2020 submission "Assessment of InSight Landing Site Predictions" to the Journal of Geophysical Research: Planets. Questions regarding these data or the paper should be directed to Matthew.P.Golombek@jpl.nasa.gov or Nathan.R.Williams@jpl.nasa.gov. This .zip archive contains data used in the analyses contained within the paper and its figures. All coordinates are reported in an equirectangular projection with a planetary radius 3396190 corresponding to the IAU/IAG Mars 2000 positive east...

An ¹⁸O/¹⁶O Study of Mesozoic and Early Tertiary Granitic Batholiths of the Southwestern North American Cordillera

George Cleve Solomon
Abundant evidence from previous studies indicates that, as long as samples are collected well away from pluton margins, the whole-rock [delta]18O value of an unaltered granitic pluton is not likely to vary by more than ±0.5 per mil from the original ¹⁸O/¹⁶O composition of its source rocks. Therefore, granitic plutons may be viewed as "remote-sensing probes" which sample deep portions of the continental crust or upper mantle, and ¹⁸O/¹⁶O studies of such plutons can provide...

Methanobacterium formicicum

Atlas of Bacterial and Archaeal Cell Structure

Ncd K401 multi 1

Ncd & K401 optogenetic motors activated by light. % different activation regions

Quantitative Model of Calcium/Calmodulin- Dependent Protein Kinase II Activation

Stefan Mihalas
Calcium/calmodulin-dependent protein kinase II (CaMKII) is a key element in the calcium second messenger cascades that lead to long term potentiation (LTP) of synaptic strength. In this thesis, I have constructed kinetic models of activation of CaMKII and measured some of the unknown parameters of the model. I used the models to elucidate mechanisms of activation of CaMKII and to study the kinetics of its activation under conditions similar to those in dendritic spines. In...

Microfluidic Devices for Genetic Analysis and Gene Expression Studies

Jian Liu
Microfluidic devices hold the promise of becoming the next-generation laboratory platforms by offering many possible benefits in chemistry, biology, and medicine. However, microfluidics is still in its infancy at present, requiring a great deal of work before it can become more than an active research field in academia. This thesis describes efforts by the author in developing microfluidic technologies for applications in genetics. Section I describes the development of miniaturized devices for genetic analysis. Successful...

Visualization of Cadherin-Cadherin Association in Living Cells

Eric Ardon Mosser
The almost universally accepted model for long-term potentiation (LTP) involves Ca2+ flux through NMDA receptors into dendritic spines. This Ca2+ influx may cause a transient Ca2+ decrease in the synaptic cleft. We hypothesize that this decrease in cleft Ca2+ may destabilize cadherin-cadherin bonds in the synapse and that this conformational change may allow synaptic cadherins to function as synaptic activity sensors. In the last decade, much effort has been devoted to understanding the structure and...

An Electron Force Field for Simulating Large Scale Excited Electron Dynamics

Julius Tsu-li Su
We introduce an electron force field (eFF) that makes simulation of large scale excited electron dynamics possible and practical. The forces acting on thousands of electrons and nuclei can be computed in less than a second on a single modern processor. Just as conventional force fields parameterize the ground state potential between nuclei, with electrons implicitly included, electron force fields parameterize the potential between nuclei and simplified electrons, with more detailed degrees of freedom implicitly...

Cranial Neural Crest Cell Migration in the Avian Embryo and the Roles of Eph-A4 and Ephrin-A5

Carole Chih-Chen Lu
The neural crest is a transient population of cells that migrate away from the dorsal neural tube in the vertebrate embryo. As the developing hindbrain constricts into rhombomeres, cranial neural crest cells migrate in three discrete streams adjacent to even-numbered rhombomeres, rhombomere 2 (r2), r4, and r6. To test the role of intrinsic versus extrinsic cues in influencing an individual cell’s trajectory, we implanted physical barriers in the chick mesoderm, distal to emerging neural crest...

Development of a Modular Strategy Towards the Total Synthesis of (+)-Pleuromutilin and Progress Towards the Synthesis of (–)-Merrilactone A

Sean S. L. Feng
Natural products have long stood as a rich source of biologically relevant molecules bearing highly functionalized and complex architectures. On one hand, they are a focal point for the development of new therapeutic agents owing to their inherent biological activities. On the other, they serve as an exciting testing ground for existing synthetic methodologies and provide opportunities for the development of new reactions. Herein, we describe a modular strategy that was employed for the total...

Activation of Cell Function; Pharmacological Agents Which Degranulate Mast Cells and Cause Skeletal Muscle to Contract

Brian Herndier
Chapter I This chapter presents a general introduction to the cellular metabolism of calcium with particular reference to the concept of calcium pools. The importance of the ionized calcium pool of the cytosol in determining the specific function of cells and tissues is discussed. A model for stimulus-release coupling in mast cells is presented. Excitation-contraction (EC) coupling in skeletal muscle is defined and the fundamental premises required for a theory on EC coupling are given....

Data Visualization 101

Kristin Briney
This is a recording from the Data Visualization 101 workshop held on 2020-05-21 over Zoom. This workshop covered how to choose the right chart type for your data and how good design choices will make your chart easier to understand. The workshop focused on visualization best practices, independent of any specific visualization software, and consisted of lecture and hands on activities.

Registration Year

  • 2020

Resource Types

  • Text
  • Audiovisual
  • Dataset
  • Image
  • Software
  • Model
  • Collection
  • Other
  • Output Management Plan


  • California Institute of Technology
  • Jet Propulsion Lab
  • Johns Hopkins University
  • University of California, Berkeley
  • University of Chicago
  • National Center for Atmospheric Research
  • Northwestern University
  • Howard Hughes Medical Institute
  • Rice University
  • Ontario Genomics Institute