Results for “dynamics”

Molecular dynamics simulation setup, execution, and trajectory analysis

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Think and work like an expert Energy Storage / Battery Scientist. Use when a task calls for Energy Storage / Battery Scientist judgment. Reasons from interfacial thermodynamics, ion transport, SEI/CEI dynamics, and cell engineering constraints (N/P and E/S ratio, mass loading) through galvanostatic cycling, dQ/dV, GITT and EIS/DRT, operando XRD, and PyBaMM/Newman models, while treating Li plating, lithium-inventory loss, transition-metal crossover, and coin-cell artifacts as first-class failure modes.

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This skill channels the strategic and empathetic reasoning of Whitney Wolfe Herd, founder and CEO of Bumble. Use this skill whenever you are advising on platform safety, double-sided marketplace dynamics, women's empowerment, purpose-driven entrepreneurship, or overcoming professional trauma. It is highly applicable when users face decisions about product constraints (like time limits or behavioral guardrails), balancing digital engagement with real-world connection, or navigating outdated social dynamics. Reach for this skill to help users shift from 'me to we,' engineer kindness into their products, and focus on core inputs rather than vanity metrics.

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Map meeting-specific power dynamics, influence ranking, and tactical recommendations.

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Classical control and system dynamics for engineered systems — feedback and closed-loop control, transfer functions and block diagrams, poles/zeros and stability, time-domain response (rise time, overshoot, settling time), PID controllers and tuning, and frequency response (Bode plots, gain and phase margin). Traces feedback control from the flyball governor to modern controllers. Use when analyzing feedback loops, designing or tuning a PID controller, assessing stability from poles or margins, or characterizing transient response of a dynamic system.

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Evaluates lock-up expiration impact with float analysis, insider selling patterns, and supply overhang assessment. Use when analyzing lock-up expirations, modeling supply dynamics, or assessing post-IPO trading patterns.

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Evaluates middle-market lending environment with competition analysis, spread trends, and deal structure evolution. Use when analyzing middle-market lending, tracking competitive dynamics, or assessing market conditions.

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Monitors private credit market evolution with AUM growth, competitive dynamics, and spread convergence with broadly syndicated markets. Use when analyzing private credit trends, tracking market evolution, or assessing competitive positioning.

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Evaluates claims trading market with trading levels, holder identification, and blocking position analysis. Use when analyzing claims markets, tracking distressed debt trading, or evaluating ad hoc group dynamics.

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Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contacts, PCA and free energy surfaces. Use this skill for protein stability under mutation, ligand binding-mode and residence-time questions, conformational sampling, membrane proteins, and disordered ensembles. Also trigger on OpenMM, MDAnalysis, mdtraj, Simulation.step, LangevinMiddleIntegrator, PDBFixer, DCD or XTC trajectory, RMSD analysis, or production MD.

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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Expert-level computational biology covering molecular dynamics simulation, protein structure prediction, systems biology, network analysis, and machine learning in biology.

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Expert-level computational chemistry knowledge. Use when working with molecular dynamics, density functional theory, force fields, quantum chemistry calculations, molecular docking, free energy calculations, or cheminformatics. Also use when the user mentions 'DFT', 'molecular dynamics', 'force field', 'AMBER', 'GROMACS', 'Gaussian', 'basis set', 'geometry optimization', 'molecular docking', 'free energy perturbation', 'QSAR', or 'cheminformatics'.

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Expert-level thermodynamics knowledge. Use when working with heat, temperature, entropy, thermodynamic laws, heat engines, refrigerators, phase transitions, statistical mechanics, or thermodynamic cycles. Also use when the user mentions 'entropy', 'enthalpy', 'Carnot', 'heat engine', 'thermodynamic cycle', 'ideal gas', 'phase transition', 'Gibbs free energy', 'specific heat', 'thermal equilibrium', or 'second law'.

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METAINFORMANT rules for directory src/metainformant/math/evolutionary_dynamics. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Run protein structure prediction, molecular design, and docking tools on Tamarind Bio without a local GPU. Guides tool selection, input validation, job submission, batch processing, and result retrieval through its REST API or MCP server.

• Predicting protein structures in the cloud
• Running binder or antibody design tools
• Submitting batches of sequences for analysis

Simulate concentration changes over time from biochemical models in SBML or Antimony, and compare fixed parameter conditions. Checks model units and exports CSV results plus COMBINE archives containing models and experiment settings, then replays them to compare results.

• Calculate concentration changes in reaction networks
• Compare baseline and altered kinetic parameters
• Inspect model units and consistency warnings

Run molecular property predictions, explore molecular shapes, and estimate how compounds bind to proteins through a cloud Python API. Process compound batches and connect modeling steps without maintaining local high-performance computing infrastructure.

• Predicting properties across a compound library
• Exploring molecular shapes and tautomeric forms
• Estimating how compounds bind to proteins

Build and optimize quantum circuits with PennyLane, including models that combine quantum circuits with PyTorch or JAX. Explore molecular energy estimation and optimization problems, validate values and gradients in simulation, and prepare tested circuits for provider plugins.

• Check quantum circuit values and gradients in simulation
• Train hybrid quantum and PyTorch or JAX models
• Estimate molecular energies with VQE

Analyze drug concentration and response data to calculate exposure, fit models of drug movement and effects, and simulate dosing schedules. Produces exploratory research results with explicit assumptions and diagnostic checks.

• Calculate exposure and half-life from concentration data
• Compare models of drug concentration over time
• Simulate dosing schedules for research