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Related Concept Videos

Lampbrush Chromosomes01:51

Lampbrush Chromosomes

In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops resemble the...
Lampbrush Chromosomes01:51

Lampbrush Chromosomes

In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops resemble the...
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...
Forces Acting on Chromosomes02:11

Forces Acting on Chromosomes

During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
Microtubules and motor proteins exert two types of forces on...
Forces Acting on Chromosomes02:11

Forces Acting on Chromosomes

During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
Microtubules and motor proteins exert two types of forces on...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer is an enzyme that can...

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  3. Chromatix: A Differentiable, Gpu-accelerated Wave-optics Library.
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  3. Chromatix: A Differentiable, Gpu-accelerated Wave-optics Library.

Related Experiment Video

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos
10:35

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Published on: October 3, 2018

Chromatix: a differentiable, GPU-accelerated wave-optics library.

Diptodip Deb1, Gert-Jan Both2, Eric Bezzam3

  • 1HHMI Janelia Research Campus, Ashburn, VA, USA. debd@janelia.hhmi.org.

Nature Methods
|June 8, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

Computational optics researchers can now use Chromatix, an open-source, GPU-accelerated, differentiable wave-optics simulation library. This tool democratizes fast, parallelized simulations, enhancing microscopy and optical system design.

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Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

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A Multilabel Single Molecule Localization Microscopy Protocol for Investigation of Chromatin in the Dense Nuclear Environment
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Area of Science:

  • Computational optics
  • Microscopy
  • Wave optics simulation

Background:

  • Computational modeling is integral to modern microscopy for inverse problems and optical system design.
  • Current methods rely on differentiable optics simulations but lack a standardized framework, hindering reusability and performance.
  • This limitation restricts the potential impact of computational optics.

Purpose of the Study:

  • Introduce Chromatix, an open-source, GPU-accelerated, differentiable wave-optics simulation library.
  • Democratize fast, parallelized simulation of diverse optical systems.
  • Expand the design space within computational optics.

Main Methods:

  • Developed Chromatix, a library built on JAX for differentiable wave-optics simulations.
  • Integrated a collection of standardized optical elements and propagation methods.
  • Leveraged graphics processing unit (GPU) acceleration for parallelized computations.

    • Main Results:

    • Chromatix provides significant speed improvements: 2-6x on a single GPU and up to 22x on 8 GPUs.
    • Demonstrated applications in snapshot microscopy, holography, and phase retrieval.
    • Enabled a broad range of applications through standardized components.

    Conclusions:

    • Chromatix offers a standardized, high-performance framework for computational optics research.
    • The library facilitates faster and more accessible optical system design and simulation.
    • Chromatix is poised to increase the impact and scope of computational optics.