#moleculardynamics

Can sand-like molecules help us map the secrets of protein structure?

Adsorption of silica oligomers on biomolecules: Structural and dynamical insights for atom probe tomography via classic molecular dynamics simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.004

CSBJ: https://www.csbj.org/

#AtomProbeTomography #MolecularDynamics #Biophysics #ProteinStructure #Nanotech #ComputationalBiology #StructuralBiology #Biomaterials #ProteinScience

Engineering Supercomputing Platforms for Biomolecular Applications

#CUDA #ROCm #Biology #Biomolecules #MolecularDynamics #HPC #Physics #Package

https://hgpu.org/?p=29954

Running 16 simulations in parallel is a very efficient way of making simulations.

It sucks however, that they all crash if one of them crashes.

#simulation #compchem #molecularDynamics #MolecularModeling

Young Scientist Award:

Petrick Heighway

for his pivotal role in the DiPOLE-100x Community Proposals measuring #XRay #diffraction at extreme pressures and temperatures at the HED-HiBEF instrument.

Combines experimental data with #MolecularDynamics simulations to provide critical insight into the nature of release pathways of shock compressed materials, kinematics of plastisticy, …

#UM25 #EuropeanXFEL

I am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:

It's on. To my #ComputationalChemistry network, I am calling on you.

The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a #PhD hashtag#candidate. The goal of the project is to understand key parameters in #semiconductor defects stability and physics (both vacancies and color centers, see for example: https://doi.org/10.1016/j.nimb.2022.12.025) through the use of
#DFT and #MolecularModeling. The end goals of the project is concerned with application for #QuantumComputing through the making of stable #qubit. Collaboration and communication with experimentalists will be part of the project.

If you're interested in #MolecularDynamics, #MonteCarlo simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as #Lammps and #QuantumEspresso. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in #physics/ #MaterialsScience / #TheoreticalChemistry. Any experience in programming using #Python, #C and the #Linux environment would be considered a plus.

The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.

Link to the offer (in french, you can ask for an english version): https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs

Trying to get back in the #moleculardynamics bandwagon. Found a #NMR structure for a relatively small neurotoxin protein bound to a small peptide that neutralizes it. No one seems to have done any MD simulations yet. Started some sims. Maybe I’ll observe something interesting worth publishing.

Is anyone doing structure prediction with #AlphaFold3 figured out an easy way to do the relaxation step that Colabfold did? I'm looking into OpenMM and Amber, and making some progress, but it seems like it will be very difficult to make it work when phosphoresidues, ions, or anything else besides standard amino acid residues are included.

#proteins #structuralbiology #moleculardynamics

In-Situ Techniques on GPU-Accelerated Data-Intensive Applications

#CUDA #HPC #Performance #MolecularDynamics

https://hgpu.org/?p=29336

RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit

#CUDA #MolecularDynamics #Physics #Package

https://hgpu.org/?p=29302

Para los que estuvieron en mi charla en la FLISoL sobre clústers de cálculo numérico, hoy largamos 729 simulaciones de 3000 partículas al clúster de una, más o menos esperamos que el mismo complete 10 corridas por día, por lo que en unos 73 días tendríamos los resultados #hpc #cluster #ciencia #md #dinamicamolecular #moleculardynamics #science #fisica #physics

Gaining Cross-Platform Parallelism for HAL’s Molecular Dynamics Package using SYCL

#SYCL #CUDA #Physics #MolecularDynamics #Package

https://hgpu.org/?p=29239

GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability

#Physics #MolecularDynamics #HPC #Performance #SYCL #Package

https://hgpu.org/?p=29198

RT by @CORDIS_EU: ️Delighted that our work to develop the BioExcel-CV19 database of Molecular Dynamics trajectories has been featured on the European Commission's Community Research and Development Information Service (CORDIS)

https://bit.ly/4bvsF9h

#moleculardynamics #database

: https://nitter.cz/BioExcelCoE/status/1754810927185088895#m

[2024-02-06 10:15 UTC]

Announcing the 2024 Les Houches-Telluride Workshop on Protein Dynamics, June 2-7

Join to interact with a great set of speakers that use experimental, theoretical and simulation approaches to decipher protein motion. A small workshop to foster exchange in an amazing setting in the French Alps.

Check the programme at https://proteindynamics2024.febsevents.org.

#Structuralbiology #NMRchat #xray #moleculardynamics #spectroscopy #diffraction #electronmicroscopy #EM #cryoEM #AFM

Molecular dynamics and multiscale modelling for sustainability

DAIMON Team - CNR-ISMN

Full time researcher in #moleculardynamics and #multiscalemodelling for sustainable materials @CNR-ISMN Bologna, Italy #Gromacs #LAMMPS

See the full job description on jobRxiv: https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-su...
https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-sustainability/?feed_id=69895

A significant challenge of biomolecular simulations are the computational limitations. A new method aims to overcome these by employing #Bayesian neural network learning models.

More details in the #preprint evaluated on @prereview

#NeuralNetwork #MolecularDynamics

https://sciety.org/articles/activity/10.1101/2023.03.25.534210?utm_source=mastodon&utm_medium=social&utm_campaign=sci_mastodon_2023_111

tenemos una PC más en el cluster de cálculo de dinámica molecular, ahi se ve corriendo el LAMMPS en 56 procesadores con Slurm WorkLoad Manager y OpenMPI #cluster #md #slurm #moleculardynamics #udelar #uruguay

`The fast multipole method (FMM), introduced by Rokhlin Jr. and Greengard has been said to be one of the top ten #algorithms of the 20th century. The FMM algorithm reduces the complexity of matrix-vector multiplication involving a certain type of dense #matrix which can arise out of many #physical #systems.`

https://en.wikipedia.org/wiki/Fast_multipole_method

#physics #simulation #molecularDynamics #MD #dynamics #differentialEquations #ODEs #PDEs #ODE #PDE #Coulomb #Coulombic #CoulombForce #CoulombInteraction

Hey #Physics #Biophysics #compchem & other friends! In my physics senior sem, my students want me to scrap a good chunk of the syllabus to write a basic #MD #MolecularDynamics engine. Any advice for doing that with advanced undergrads? Looking to make sure they get lots of good physics along the way

New paper. A total of about 10 years of work.

Approximately 40% of all proteins are intrinsically disordered or contain intrinsically disordered regions. So far, it was widely believed that these regions always had a random coil secondary structure. We show that this is not necessarily the case.

We applied the replica method to a generalized Langevin equation to describe the structure of AXR3, which is a co-receptor of the plant growth hormone auxin, and found that it adopts a number of distinct, different tertiary structures. Of these, two are particularly stable, almost equally probable, and account for 90% of the conformations. The results are confirmed by NMR spectroscopy and circular dichroism experiments. This shows that intrinsic disorder does not always mean a constantly disordered structure, such as a random coil or a Gaussian self-avoiding walk. Rather, disorder can arise as an ensemble effect of a glassy energy landscape, in which a protein can exist in a mixture of separate folded structures, with an energy barrier that may also induce symmetry breaking and the effective loss of ergodicity, depending on its height.

The fact that the first fully characterized example of such cases is a plant protein from the auxin system is an added bonus.

#computationalbiology #biology #biophysics #statistical #physics #Complexity #ComplexSystems #plantbiology #hormones #auxin #moleculardynamics #simulation #NMR #circulardichroism #structure #disorder #IDP #IDR

https://www.pnas.org/doi/10.1073/pnas.2221286120