Visual Interactive Analysis of Molecular Dynamics v0.1.39 released
VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed at the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudementary script language that is used to declare operations which are performed over the frames of the trajectory. The results can then be viewed in the different windows exposed in the application.
https://github.com/scanberg/viamd
VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed at the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudementary script language that is used to declare operations which are performed over the frames of the trajectory. The results can then be viewed in the different windows exposed in the application.
https://github.com/scanberg/viamd
❤12
Extreme‑Scale Electronic Structure Engine Announced
A new computational platform, the Extreme‑scale Electronic Structure System (EXESS), claims large performance gains for electronic structure calculations via aggressive parallelization and fragmentation strategies, enabling large‑molecule quantum simulations that previously required weeks to run.
https://www.livescience.com/technology/computing/ultrafast-quantum-chemistry-engine-could-speed-up-the-development-of-new-medicines-and-materials
Access here: https://exess.qdx.co/try
A new computational platform, the Extreme‑scale Electronic Structure System (EXESS), claims large performance gains for electronic structure calculations via aggressive parallelization and fragmentation strategies, enabling large‑molecule quantum simulations that previously required weeks to run.
https://www.livescience.com/technology/computing/ultrafast-quantum-chemistry-engine-could-speed-up-the-development-of-new-medicines-and-materials
Access here: https://exess.qdx.co/try
Live Science
Ultrafast quantum chemistry engine could speed up the development of new medicines and materials
The powerful software can reduce the time needed to simulate reactions with large molecules from weeks to just minutes.
❤2
LightCone: A Molecule Visualization and Editing Tool
Demo video here: https://youtu.be/B86dnn7rHNo
Access the app here: https://lightcone.quanta-bricks.com
Demo video here: https://youtu.be/B86dnn7rHNo
Access the app here: https://lightcone.quanta-bricks.com
❤7
Half‑Möbius molecular topology experimentally realized and validated computationally
Researchers have synthesized the first molecule exhibiting a half‑Möbius electronic topology, an unusual orbital topology where a cyclic π system contains a half‑twist. Electronic‑structure calculations and quantum‑computer simulations were required because standard density functional theory struggled to describe the system reliably.
https://www.chemistryworld.com/news/first-half-m%C3%B6bius-molecule-made/4023073.article
Researchers have synthesized the first molecule exhibiting a half‑Möbius electronic topology, an unusual orbital topology where a cyclic π system contains a half‑twist. Electronic‑structure calculations and quantum‑computer simulations were required because standard density functional theory struggled to describe the system reliably.
https://www.chemistryworld.com/news/first-half-m%C3%B6bius-molecule-made/4023073.article
Chemistry World
First half-Möbius molecule made
Twisted structure is an unprecedented case of a compound that becomes aromatic by breaking its own symmetry
❤7🔥7
Large‑scale whole‑cell simulation reaches new level of molecular detail
A team has simulated a minimal living cell (JCVI‑syn3A) across a full cell cycle, tracking thousands of interacting molecular species simultaneously using multiscale computational approaches.
https://chemistry.illinois.edu/news/2026-03-09/team-simulates-living-cell-grows-and-divides
A team has simulated a minimal living cell (JCVI‑syn3A) across a full cell cycle, tracking thousands of interacting molecular species simultaneously using multiscale computational approaches.
https://chemistry.illinois.edu/news/2026-03-09/team-simulates-living-cell-grows-and-divides
chemistry.illinois.edu
Team simulates a living cell that grows and divides | Department of Chemistry | Illinois
Image
❤5🔥2
Chebifier: automating semantic classification in ChEBI to accelerate data-driven discovery
Connecting chemical structural representations with meaningful categories and semantic annotations representing existing knowledge enables data-driven digital discovery from chemistry data. Ontologies are semantic annotation resources that provide definitions and a classification hierarchy for a domain. They are widely used throughout the life sciences. ChEBI is a large-scale ontology for the domain of biologically interesting chemistry that connects representations of chemical structures with meaningful chemical and biological categories. Classifying novel molecular structures into ontologies such as ChEBI has been a longstanding objective for data scientific methods, but the approaches that have been developed to date are limited in several ways: they are not able to expand as the ontology expands without manual intervention, and they are not able to learn from continuously expanding data. We have developed an approach for automated classification of chemicals in the ChEBI ontology based on a neuro-symbolic AI technique that harnesses the ontology itself to create the learning system. We provide this system as a publicly available tool, Chebifier, and as an API, ChEB-AI. We here evaluate our approach and show how it constitutes an advance towards a continuously learning semantic system for chemical knowledge discovery.
read the paper: https://pubs.rsc.org/en/content/articlelanding/2024/dd/d3dd00238a
Use the service: https://chebifier.hastingslab.org
Connecting chemical structural representations with meaningful categories and semantic annotations representing existing knowledge enables data-driven digital discovery from chemistry data. Ontologies are semantic annotation resources that provide definitions and a classification hierarchy for a domain. They are widely used throughout the life sciences. ChEBI is a large-scale ontology for the domain of biologically interesting chemistry that connects representations of chemical structures with meaningful chemical and biological categories. Classifying novel molecular structures into ontologies such as ChEBI has been a longstanding objective for data scientific methods, but the approaches that have been developed to date are limited in several ways: they are not able to expand as the ontology expands without manual intervention, and they are not able to learn from continuously expanding data. We have developed an approach for automated classification of chemicals in the ChEBI ontology based on a neuro-symbolic AI technique that harnesses the ontology itself to create the learning system. We provide this system as a publicly available tool, Chebifier, and as an API, ChEB-AI. We here evaluate our approach and show how it constitutes an advance towards a continuously learning semantic system for chemical knowledge discovery.
read the paper: https://pubs.rsc.org/en/content/articlelanding/2024/dd/d3dd00238a
Use the service: https://chebifier.hastingslab.org
pubs.rsc.org
Chebifier: automating semantic classification in ChEBI to accelerate data-driven discovery
Connecting chemical structural representations with meaningful categories and semantic annotations representing existing knowledge enables data-driven digital discovery from chemistry data. Ontologies are semantic annotation resources that provide definitions…
❤3
[Open Access] Precise Quantum Chemistry calculations with few Slater Determinants
Demonstrates that a compact set of optimized non‑orthogonal determinants can achieve near‑state‑of‑the‑art accuracy in correlated electronic structure calculations.
https://www.nature.com/articles/s41467-026-70255-z
Demonstrates that a compact set of optimized non‑orthogonal determinants can achieve near‑state‑of‑the‑art accuracy in correlated electronic structure calculations.
https://www.nature.com/articles/s41467-026-70255-z
Nature
Precise Quantum Chemistry calculations with few Slater Determinants
Nature Communications - Accurate description of electronic wave functions typically requires large numbers of Slater determinants. Here, the authors develop an optimization method that achieves...
❤5👀2
Forwarded from PhDFinder
📢 Austria – Postdoc Position in Materials Theory at University of Salzburg
🏛 University: Paris Lodron University of Salzburg
🌍 Country: Austria
🎓 Fields:
Physics, Chemistry, Materials Science, Computational Science, Physical Chemistry
Are you passionate about advancing the theoretical understanding of materials and eager to contribute to groundbreaking research in a collaborative, international environment?
The position is based within the Materials Theory group, focusing on the chemistry and physics of materials. Materials theory is a cornerstone of modern science and technology, enabling the prediction and understanding of material properties at the atomic and electronic levels. Research in this area underpins advances in electronics, energy storage, catalysis, and sustainable materials.
🔗 Find out more and Apply Now:
⚠️ Android users: If it doesn't open, use "Open in browser"
https://phdfinder.com/2026/03/30/austria-postdoc-position-in-materials-theory-at-university-of-salzburg/?utm_source=telegram&utm_medium=social&utm_campaign=job_post
━━━━━━━━━━━━━━━
🏛 University: Paris Lodron University of Salzburg
🌍 Country: Austria
🎓 Fields:
Physics, Chemistry, Materials Science, Computational Science, Physical Chemistry
Are you passionate about advancing the theoretical understanding of materials and eager to contribute to groundbreaking research in a collaborative, international environment?
The position is based within the Materials Theory group, focusing on the chemistry and physics of materials. Materials theory is a cornerstone of modern science and technology, enabling the prediction and understanding of material properties at the atomic and electronic levels. Research in this area underpins advances in electronics, energy storage, catalysis, and sustainable materials.
🔗 Find out more and Apply Now:
⚠️ Android users: If it doesn't open, use "Open in browser"
https://phdfinder.com/2026/03/30/austria-postdoc-position-in-materials-theory-at-university-of-salzburg/?utm_source=telegram&utm_medium=social&utm_campaign=job_post
━━━━━━━━━━━━━━━
PhDFinder
[Expired] Austria – Postdoc Position in Materials Theory at University of Salzburg - PhDFinder
⛔ This position is no longer available.
👍5❤3🙏1
Pairs of atoms observed existing in two places at once for the first time https://share.google/PLlPCmrarZmjuikM6
phys.org
Pairs of atoms observed existing in two places at once for the first time
Quantum physicists at ANU have observed atoms entangled in motion. "It's really weird for us to think that this is how the universe works," says Dr. Sean Hodgman from the ANU Research School of Physics. ...
❤3👀2
AVOGADRO 2 IS HERE!!!
Rebuilt from the ground up: fast modern rendering, improved stability, designed for the next generation of molecular, biomolecule, and materials research & education. 🧪 ⚗️
https://avogadro.cc/install/
https://discuss.avogadro.cc
#opensource #openscience #compchem
Rebuilt from the ground up: fast modern rendering, improved stability, designed for the next generation of molecular, biomolecule, and materials research & education. 🧪 ⚗️
https://avogadro.cc/install/
https://discuss.avogadro.cc
#opensource #openscience #compchem
❤15
Forwarded from Quantum Chemistry And Stuff
A Molecular Dynamics Bridge Between Small and Large Scales
A special issue of International Journal of Molecular Sciences (IJMS).
Dear Colleagues,
Molecular dynamics is a powerful modeling tool for matter, capable of simulating both equilibrium and non-equilibrium systems with atomistic resolution across a wide range of particle numbers: from a few-atomic systems to millions of atoms, representing materials and biochemical systems, and time intervals from a few tens of femtoseconds to microseconds. This Special Issue of the International Journal of Molecular Sciences will delve into new methodological developments and case studies in areas such as, but not limited to, nuclear quantum effects in molecular dynamics, enhanced sampling methods for rare events, photochemical and radiation chemistry simulations using molecular dynamics, analysis tools, and many more. We welcome papers that use molecular dynamics with a range of potential energy surfaces, including ab initio, classical force fields, machine learning potentials, and their combinations.
Dr. Denis S. Tikhonov
Guest Editor
More details can be found here:
https://www.mdpi.com/journal/ijms/special_issues/0MOCRS279R
Image credits @jette.ki
A special issue of International Journal of Molecular Sciences (IJMS).
Dear Colleagues,
Molecular dynamics is a powerful modeling tool for matter, capable of simulating both equilibrium and non-equilibrium systems with atomistic resolution across a wide range of particle numbers: from a few-atomic systems to millions of atoms, representing materials and biochemical systems, and time intervals from a few tens of femtoseconds to microseconds. This Special Issue of the International Journal of Molecular Sciences will delve into new methodological developments and case studies in areas such as, but not limited to, nuclear quantum effects in molecular dynamics, enhanced sampling methods for rare events, photochemical and radiation chemistry simulations using molecular dynamics, analysis tools, and many more. We welcome papers that use molecular dynamics with a range of potential energy surfaces, including ab initio, classical force fields, machine learning potentials, and their combinations.
Dr. Denis S. Tikhonov
Guest Editor
More details can be found here:
https://www.mdpi.com/journal/ijms/special_issues/0MOCRS279R
Image credits @jette.ki
❤6👍3
stable_and_accurate_orbital_free_density_functional_theory_powered.pdf
8.4 MB
Stable and Accurate Orbital-Free Density Functional Theory Powered by Machine Learning
First neural-network kinetic energy functional that makes orbital-free DFT both chemically accurate and variationally stable for diverse organic molecules, including drug-like systems. Trained on perturbed densities to guarantee convergence. Widely discussed in Q1 2026; model and code publicly available.
First neural-network kinetic energy functional that makes orbital-free DFT both chemically accurate and variationally stable for diverse organic molecules, including drug-like systems. Trained on perturbed densities to guarantee convergence. Widely discussed in Q1 2026; model and code publicly available.
❤9
🔬 Join the TURBOMOLE development team!
A PhD position in computational chemistry is open in the Quantum Chemistry Group of Prof. Dr. Christof Hättig at Ruhr-Universität Bochum.
🎯 The project: Develop advanced coupled-cluster methods for electronically excited states in solution — with direct applications to emission and phosphorescence spectra of OLED and TADF materials.
💻 As part of this project, you will contribute directly to TURBOMOLE, implementing cutting-edge coupled-cluster response theory and modern solvation models into one of the world's leading quantum chemistry packages.
🌐 The position is embedded in the RESOLV Cluster of Excellence, offering an outstanding interdisciplinary research environment with strong international collaborations.
📋 Key details:
▸ Start: October 2026
▸ Duration: 3 years (E13 TV-L, 67%)
▸ Application deadline: July 31, 2026
👉 Apply here: https://lnkd.in/d5dPPyJt
🔎 Source: https://shorturl.at/IHCwY
A PhD position in computational chemistry is open in the Quantum Chemistry Group of Prof. Dr. Christof Hättig at Ruhr-Universität Bochum.
🎯 The project: Develop advanced coupled-cluster methods for electronically excited states in solution — with direct applications to emission and phosphorescence spectra of OLED and TADF materials.
💻 As part of this project, you will contribute directly to TURBOMOLE, implementing cutting-edge coupled-cluster response theory and modern solvation models into one of the world's leading quantum chemistry packages.
🌐 The position is embedded in the RESOLV Cluster of Excellence, offering an outstanding interdisciplinary research environment with strong international collaborations.
📋 Key details:
▸ Start: October 2026
▸ Duration: 3 years (E13 TV-L, 67%)
▸ Application deadline: July 31, 2026
👉 Apply here: https://lnkd.in/d5dPPyJt
🔎 Source: https://shorturl.at/IHCwY
❤5😍1