FreeDTS
FreeDTS is software to perform computational research on biomembranes at messocpic length-scale.
https://github.com/weria-pezeshkian/FreeDTS
FreeDTS is software to perform computational research on biomembranes at messocpic length-scale.
https://github.com/weria-pezeshkian/FreeDTS
GitHub
GitHub - weria-pezeshkian/FreeDTS: a package to simulate fluid surfaces and biomembranes
a package to simulate fluid surfaces and biomembranes - weria-pezeshkian/FreeDTS
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Elk version 8.8.26 has just been released
———————————————————-
This version features molecular dynamics using atomic trajectories
determined from the Hellman-Feynman + IBS forces. See the examples in
the elk/examples/molecular-dynamics directory for details. This
technique can also be used as a simple structural prediction method
using simulated annealing. Furthermore, the molecular dynamics forces
can be subsequently used in a TDDFT Ehrenfest calculation, although this
should be considered an experimental feature.
The new version is faster and more stable for most tasks.
Also included are examples of the electron-phonon coupled Bogoliubov
equations as described in Phys. Rev. B 105, 174509 (2022). See the
elk/examples/Bogoliubov directory.
https://sourceforge.net/projects/elk/
———————————————————-
This version features molecular dynamics using atomic trajectories
determined from the Hellman-Feynman + IBS forces. See the examples in
the elk/examples/molecular-dynamics directory for details. This
technique can also be used as a simple structural prediction method
using simulated annealing. Furthermore, the molecular dynamics forces
can be subsequently used in a TDDFT Ehrenfest calculation, although this
should be considered an experimental feature.
The new version is faster and more stable for most tasks.
Also included are examples of the electron-phonon coupled Bogoliubov
equations as described in Phys. Rev. B 105, 174509 (2022). See the
elk/examples/Bogoliubov directory.
https://sourceforge.net/projects/elk/
SourceForge
Elk
Download Elk for free. An all-electron full-potential linearised augmented-planewave (FP-LAPW) code. Designed to be as developer friendly as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.
👍2
Scientists Discover a New Class of “Molecular Motors”
https://scitechdaily.com/scientists-discover-a-new-class-of-molecular-motors/
https://scitechdaily.com/scientists-discover-a-new-class-of-molecular-motors/
SciTechDaily
Scientists Discover a New Class of “Molecular Motors”
Cells possess a remarkable ability to organize their interiors using minuscule protein machines known as molecular motors, which generate directed motion. Most molecular motors rely on a common form of chemical energy, ATP, to function. Recently, a team of…
Theoretical Physicists Discover Why Optical Cavities Slow Down Chemical Reactions
https://scitechdaily.com/theoretical-physicists-discover-why-optical-cavities-slow-down-chemical-reactions/
https://scitechdaily.com/theoretical-physicists-discover-why-optical-cavities-slow-down-chemical-reactions/
SciTechDaily
Theoretical Physicists Discover Why Optical Cavities Slow Down Chemical Reactions
Scientists have discovered why chemical reactions are slowed down in mirrored cavities, where molecules interact with light. The team used Quantum-Electrodynamical Density-Functional Theory to find that the conditions inside the optical cavity affected the…
Beyond the Spectrum: Machine Learning Unlocks Predictive Power in Organic Chemistry Research
https://scitechdaily.com/beyond-the-spectrum-machine-learning-unlocks-predictive-power-in-organic-chemistry-research/
https://scitechdaily.com/beyond-the-spectrum-machine-learning-unlocks-predictive-power-in-organic-chemistry-research/
SciTechDaily
Beyond the Spectrum: Machine Learning Unlocks Predictive Power in Organic Chemistry Research
Scientists have developed a machine-learning algorithm that predicts electron energy levels in organic molecules. This breakthrough, trained on a database of over 22,000 molecules, could accelerate the design of functional molecules like pharmaceuticals.…
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Chemfp 4.1 was released
Chemfp - Fast cheminformatics fingerprint search, anywhere you use Python
📄 Chemfp is an analytics platform for cheminformatics fingerprints. It contains command-line tools and an extensive Python library for fingerprint generation, high-performance similarity search, diversity selection, and exploratory research.
# Why chemfp?
* Do you want single-threaded search of 1M 1024-bit fingerprints in under 10 milliseconds?
* Do you want to make a sparse similarity matrix from 1M 2048-bit fingerprints in less than 30 minutes on a four core machine?
* Do you want to include fingerprint similarity results in your Python web application?
... with fast reload times during development, and without the complexity of using a dedicated search server?
* Do you want fast Butina clustering? Or MaxMin or sphere exclusion diversity selection?
* Do you work with fingerprints from multiple chemistry toolkits, or have custom fingerprint types?
* Do you want command-line tools with sub-second similarity search times?
* Do you program in Python and want to write new fingerprint analysis programs?
* Do you want the option to have the source code with no time-based licensing?
🔗 https://chemfp.com/
Chemfp - Fast cheminformatics fingerprint search, anywhere you use Python
📄 Chemfp is an analytics platform for cheminformatics fingerprints. It contains command-line tools and an extensive Python library for fingerprint generation, high-performance similarity search, diversity selection, and exploratory research.
# Why chemfp?
* Do you want single-threaded search of 1M 1024-bit fingerprints in under 10 milliseconds?
* Do you want to make a sparse similarity matrix from 1M 2048-bit fingerprints in less than 30 minutes on a four core machine?
* Do you want to include fingerprint similarity results in your Python web application?
... with fast reload times during development, and without the complexity of using a dedicated search server?
* Do you want fast Butina clustering? Or MaxMin or sphere exclusion diversity selection?
* Do you work with fingerprints from multiple chemistry toolkits, or have custom fingerprint types?
* Do you want command-line tools with sub-second similarity search times?
* Do you program in Python and want to write new fingerprint analysis programs?
* Do you want the option to have the source code with no time-based licensing?
🔗 https://chemfp.com/
Quantum Chemistry Package 2023 for Maple Released
The team at RDMChem hopes that you are doing well. Today we are excited to announce the launch of the 2023 Edition of the Quantum Chemistry Package for Maple 2023! The Maple Quantum Chemistry Package 2023 provides a powerful, parallel platform for quantum chemistry calculations that directly integrates as an add-on package into the Maple 2023 environment. It is optimized for both research and education. The Add-on Package (also known as Toolbox) includes density functional theory and wave function methods as well as advanced two-electron reduced density matrix (2-RDM) theories. It is available on Windows, MacOS, and Linux.
The 2023 Package has significant new features and enhancements including:
* New Subpackage for Quantum Computing
* Literature Search via 40+ Million Articles
* Fly-through Molecule Animations
* Custom Hamiltonians in Variational 2-RDM
* Geometries from SMILES Formulas
* Enhanced Editing of Molecular Plots
* Explore Enhancements throughout the Package
https://www.rdmchem.com/
The team at RDMChem hopes that you are doing well. Today we are excited to announce the launch of the 2023 Edition of the Quantum Chemistry Package for Maple 2023! The Maple Quantum Chemistry Package 2023 provides a powerful, parallel platform for quantum chemistry calculations that directly integrates as an add-on package into the Maple 2023 environment. It is optimized for both research and education. The Add-on Package (also known as Toolbox) includes density functional theory and wave function methods as well as advanced two-electron reduced density matrix (2-RDM) theories. It is available on Windows, MacOS, and Linux.
The 2023 Package has significant new features and enhancements including:
* New Subpackage for Quantum Computing
* Literature Search via 40+ Million Articles
* Fly-through Molecule Animations
* Custom Hamiltonians in Variational 2-RDM
* Geometries from SMILES Formulas
* Enhanced Editing of Molecular Plots
* Explore Enhancements throughout the Package
https://www.rdmchem.com/
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The Potential of Artificial Intelligence in Molecular Dynamics
https://ts2.space/en/the-potential-of-artificial-intelligence-in-molecular-dynamics/
https://ts2.space/en/the-potential-of-artificial-intelligence-in-molecular-dynamics/
TS2 SPACE
The Potential of Artificial Intelligence in Molecular Dynamics
The Potential of Artificial Intelligence in Molecular Dynamics TS2 SPACE
Forwarded from Lets Learn Bio-IT School 🇫🇷🇮🇳
Are you a biologist looking to learn R from scratch?
Then, our upcoming two days international virtual workshop ennoscriptd Introduction to R for Biologists is for you,
🗓 Scheduled on 24-25 June 2023.
》It covers the basics of R programming language, data structures, operators, and control structures.
》You will work with GenomicRanges & Biostrings packages and visualise NGS data with Bioconductor.
》You will also learn how to create publication-quality plots using ggplot2 and utilise Bioconductor packages for data analysis.
》The workshop will include both theory and hands-on sessions, so you will have the opportunity to practice your newly acquired skills.
🎁Benefits:
》Provided with participation certificate
》Recorded videos are provided
👩🎓Eligibility:
The program is interdisciplinary * and open to all interested participants with no programming knowledge.
💰Check the flyer for Fee & other details
👨💻Register now at our website:
https://www.nyberman.com/home#h.8zbwlts0r6hb
📢➖➖➖➖➖
@bioinfo_channel
Then, our upcoming two days international virtual workshop ennoscriptd Introduction to R for Biologists is for you,
🗓 Scheduled on 24-25 June 2023.
》It covers the basics of R programming language, data structures, operators, and control structures.
》You will work with GenomicRanges & Biostrings packages and visualise NGS data with Bioconductor.
》You will also learn how to create publication-quality plots using ggplot2 and utilise Bioconductor packages for data analysis.
》The workshop will include both theory and hands-on sessions, so you will have the opportunity to practice your newly acquired skills.
🎁Benefits:
》Provided with participation certificate
》Recorded videos are provided
👩🎓Eligibility:
The program is interdisciplinary * and open to all interested participants with no programming knowledge.
💰Check the flyer for Fee & other details
👨💻Register now at our website:
https://www.nyberman.com/home#h.8zbwlts0r6hb
📢➖➖➖➖➖
@bioinfo_channel
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‘Almost magical’: chemists can now move single atoms in and out of a molecule’s core
https://www.nature.com/articles/d41586-023-01735-1
https://www.nature.com/articles/d41586-023-01735-1
Nature
‘Almost magical’: chemists can now move single atoms in and out of a molecule’s core
Nature - An explosion of skeletal editing methods to insert, delete or swap individual atoms in molecular backbones could accelerate drug discovery.
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World's First X-Ray of a Single Atom Reveals Chemistry on The Smallest Level : ScienceAlert
https://www.sciencealert.com/worlds-first-x-ray-of-a-single-atom-reveals-chemistry-on-the-smallest-level
https://www.sciencealert.com/worlds-first-x-ray-of-a-single-atom-reveals-chemistry-on-the-smallest-level
ScienceAlert
World's First X-Ray of a Single Atom Reveals Chemistry on The Smallest Level
Oh no! Tiny skeletons!
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Physicists develop powerful alternative to dynamic density functional theory
https://phys.org/news/2023-06-physicists-powerful-alternative-dynamic-density.html
https://phys.org/news/2023-06-physicists-powerful-alternative-dynamic-density.html
phys.org
Physicists develop powerful alternative to dynamic density functional theory
Living organisms, ecosystems and the planet Earth are, from a physics point of view, examples of extraordinarily large and complex systems that are not in thermal equilibrium. To physically describe non-equilibrium ...
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Scientists develop artificial molecules that behave like real ones
https://phys.org/news/2023-06-scientists-artificial-molecules-real.html
https://phys.org/news/2023-06-scientists-artificial-molecules-real.html
phys.org
Scientists develop artificial molecules that behave like real ones
Scientists from the Radboud University have developed synthetic molecules that resemble real organic molecules. A collaboration of researchers, led by Alex Khajetoorians and Daniel Wegner, can now simulate ...
Implications of no-free-lunch theorems
https://phys.org/news/2023-06-implications-no-free-lunch-theorems.html
https://phys.org/news/2023-06-implications-no-free-lunch-theorems.html
phys.org
Implications of no-free-lunch theorems
In the 18th century, the philosopher David Hume observed that induction—inferring the future based on what's happened in the past—can never be reliable. In 1997, SFI Professor David Wolpert with his ...