36 skills found · Page 1 of 2
mat10d / EvolveProThis is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.
patrickbryant1 / EvoBindIn silico directed evolution of peptide binders with AlphaFold
vynect / Era Connect🚀 ERA Connect by VYNECT™ — The evolution of secure WhatsApp automation ERA Connect is part of the VYNECT™ ecosystem, offering a premium solution for safe, ethical WhatsApp automation and testing using direct WebSocket communication. Automate conversations, simulate interactions, and manage messages with maximum speed, security, and stability
ai4protein / ProSST🧬 Advanced hybrid language model for directed protein evolution. (NeurIPS 2024)
NatLabRockies / EvoProtGradDirected evolution of proteins in sequence space with gradients
ai4protein / ProtSSN🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2025).
jsunn-y / ALDEActive Learning-Assisted Directed Evolution for Protein Engineering
lucidrains / Transformer Directed EvolutionExplorations into whether a transformer with RL can direct a genetic algorithm to converge faster
ShelvanLee / XFEM# XFEM_Fracture2D ### Description This is a Matlab program that can be used to solve fracture problems involving arbitrary multiple crack propagations in a 2D linear-elastic solid based on the principle of minimum potential energy. The extended finite element method is used to discretise the solid continuum considering cracks as discontinuities in the displacement field. To this end, a strong discontinuity enrichment and a square-root singular crack tip enrichment are used to describe each crack. Several crack growth criteria are available to determine the evolution of cracks over time; apart from the classic maximum tension (or hoop-stress) criterion, the minimum total energy criterion and the local symmetry criterion are implemented implicitly with respect to the discrete time-stepping. ### Key features * *Fast:* The stiffness matrix and the force vector (i.e. the equations' system) and the enrichment tracking data structures are updated at each time step only with respect to the changes in the fracture topology. This ultimately results in the major part of the computational expense in the solution to the linear system of equations rather than in the post-processing of the solution or in the assembly and updating of the equations. As Matlab offers fast and robust direct solvers, the computational times are reasonably fast. * *Robust.* Suitable for multiple crack propagations with intersections. Furthermore, the stress intensity factors are computed robustly via the interaction integral approach (with the inclusion of the terms to account for crack surface pressure, residual stresses or strains). The minimum total energy criterion and the principle of local symmetry are implemented implicitly in time. The energy release rates are computed based on the stiffness derivative approach using algebraic differentiation (rather than finite differencing of the potential energy). On the other hand, the crack growth direction based on the local symmetry criterion is determined such that the local mode-II stress intensity factor vanishes; the change in a crack tip kink angle is approximated using the ratio of the crack tip stress intensity factors. * *Easy to run.* Each job has its own input files which are independent form those of all other jobs. The code especially lends itself to running parametric studies. Various results can be saved relating to the fracture geometry, fracture mechanics parameters, and the elastic fields in the solid domain. Extensive visualisation library is available for plotting results. ### Instructions 1. Get started by running the demo to showcase some of the capabilities of the program and to determine if it can be useful for you. At the Matlab's command line enter: ```Matlab >> RUN_JOBS.m ``` This will execute a series of jobs located inside the *jobs directory* `./JOBS_LIBRARY/`. These jobs do not take very long to execute (around 5 minutes in total). 2. Subsequently, you can pick one of the jobs inside `./JOBS_LIBRARY/` by defining the job title: ```Matlab >> job_title = 'several_cracks/edge/vertical_tension' ``` 3. Then you can open all the relevant scripts for this job as follows: ```Matlab >> open_job ``` The following input scripts for the *job* will be open in the Matlab's editor: 1. `JOB_MAIN.m`: This is the job's main script. It is called when executing `RUN_JOB` (or `RUN_JOBS`) and acts like a wrapper. Notably, it can serve as a convenient interface to run parametric studies and to save intermediate simulation results. 2. `Input_Scope.m`: This defines the scope of the simulation. From which crack growth criteria to use, to what to compute and what results to show via plots and/or movies. To put it simply, the script is a bunch of "switches" that tell the program what the user wants to be done. 3. `Input_Material.m`: Defines the material's elastic properties in different regions or layers (called "phases") of the computational domain. Moreover, it defines the fracture toughness of the material (assumed to be constant in all material phases). 4. `Input_Crack.m`: Defines the initial crack geometry. 5. `Input_BC.m`: Defines boundary conditions, such as displacements, tractions, crack surface pressure (assumed to be constant in all cracks), body loads (e.g. gravity, pre-stress or pre-strain). 6. `Mesh_make.m`: In-house structured mesh generator for rectangular domains using either linear triangle or bilinear quadrilateral elements. It is possible to mesh horizontal layers using different mesh sizes. 7. `Mesh_read.m`: Gmsh based mesh reader for version-1 mesh files. Of course you can use your own mesh reader provided the output variables are of the correct format (see later). 8. `Mesh_file.m`: Specifies the mesh input file (.msh). At the moment, only Gmsh mesh files of version-1 are allowed. ### Mesh_file.m A mesh file needs to be able to output the following data or variables: * `mNdCrd`: Node coordinates, size = `[nNdStd, 2]` * `mLNodS`: Element connectivities, size = `[nElemn,nLNodS]` * `vElPhz`: Element material phase (or region) ID's, size = `[nElemn,1]` * `cBCNod`: cell of boundary nodes, cell size = `{nBound,1}`, cell element size = `[nBnNod,2]` Example mesh files are located in `./JOBS_LIBRARY/`. Gmsh version-1 file format is described [here](http://www.manpagez.com/info/gmsh/gmsh-2.4.0/gmsh_60.php). ### Additional notes * global variables are defined in `.\Routines_AuxInput\Declare_Global.m` * External libraries are `.\Other_Libs\distmesh` and `.\Other_Libs\mesh2d` ### References Two external meshing libraries are used for the local mesh refinement and remeshing at the crack tip during crack propagation or prior to a crack intersection with another crack or with a boundary of the domain. Specifically, these libraries, which are located in `.\Other_Libs\`, are the following: * [*mesh2d*](https://people.sc.fsu.edu/~jburkardt/m_src/mesh2d/mesh2d.html) by Darren Engwirda * [*distmesh*](http://persson.berkeley.edu/distmesh/) by Per-Olof Persson and Gilbert Strang. ### Issues and Support For support or questions please email [sutula.danas@gmail.com](mailto:sutula.danas@gmail.com). ### Authors Danas Sutula, University of Luxembourg, Luxembourg. If you find this code useful, we kindly ask that you consider citing us. * [Minimum energy multiple crack propagation](http://hdl.handle.net/10993/29414)
HySonLab / Directed EvolutionProtein Design by Machine Learning guided Directed Evolution
MicroResearchLab / AMP Potency Prediction EvoGradientA PyTorch implementation of "Automatic Identification and Virtual Directed Evolution of Antimicrobial Peptides with Explainable Deep Learning".
HySonLab / LatentDELatentDE: Latent-based Directed Evolution for Protein Sequence Design
Wang-Lin-boop / OuroborosAn official implementation of "Directed Chemical Evolution via Navigating Molecular Encoding Space.", which is a foundational model to bridge the gap between representation learning and generative AI models in drug discovery.
GrandpaEJ / AdvanceggAdvanceGG is a modern, high-performance 2D graphics library for Go — a direct fork and evolution of gg.
wwwtyro / Spaceship 2dCreate 2D spaceship diffuse, normal, depth, and position sprites with ambient occlusion through directed evolution.
kamerlinlab / CadeeCADEE: Computer-Aided Directed Evolution of Enzymes
eugene / Prot Bo 0:pill: Guiding directed protein evolution with Bayesian Optimization - First Steps :pill:
fhalab / SSMuLACode base for "Evaluation of Machine Learning-Assisted Directed Evolution Across Diverse Combinatorial Landscapes"
pemami4911 / PpdeOfficial repository for "Plug & Play Directed Evolution for Proteins with Gradient-Based Discrete MCMC"
fhalab / EnzymeEngineeringDBDatabase for directed evolution and enzyme engineering
