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Biophysics of Biomolecules Training | Thermodynamics (ΔG/ΔH/ΔS) , PMFs & Kinetics (MSMs, k_on/k_off)

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Proteomics, Structural Bioinformatics, Molecular Modeling >> Biophysics of Biomolecules Training | Thermodynamics (ΔG/ΔH/ΔS) , PMFs & Kinetics (MSMs, k_on/k_off)

Biophysics of Biomolecules: Thermodynamics & Kinetics — Hands-on

Bridge simulation and experiment to extract rigorous thermodynamics and kinetics for biomolecular processes. Learn to compute free energies and rate constants from simulations and interpret them alongside ITC/SPR/thermal data in transparent, reproducible workflows.

Biophysics of Biomolecules: Thermodynamics & Kinetics
Help Desk · WhatsApp
Session 1
Fee: Rs 6300
Thermodynamics Foundations & Binding
  • State functions & ensembles; ΔG, ΔH, ΔS and partition functions
    • Theory
  • Binding thermodynamics & linking Kd to ΔG (ITC/van’t Hoff)
    • ITC/SPR interpretation van’t Hoff/Eyring plots
  • Simulation observables → thermodynamic quantities
    • alchemical/endpoint overview convergence sanity
Session 2
Fee: Rs 8400
Kinetics, MSMs & Rate Theory
  • Transition-state theory, Kramers, and reaction coordinates
    • barrier crossing committor concepts
  • Markov State Models (MSMs) for kinetics from MD
    • PyEMMA/MSMBuilder implied timescales MFPT/residence time
  • kon/koff estimation & uncertainty
    • bootstraps/CI model diagnostics
Session 3
Fee: Rs 11200
PMFs & Enhanced Sampling
  • Potential of mean force (PMF) along collective variables
    • umbrella sampling WHAM integration
  • Metadynamics & biasing strategies with PLUMED
    • well-tempered meta bias deposition & recovery
  • Toolchain & practice
    • GROMACS/AMBER PLUMED MDTraj/MDAnalysis
Session 4
Fee: Rs 14000
Mini Capstone: ΔG/ΔH/ΔS & k Extraction
  • From MD to PMF and MSM: compute ΔG and rate constants for a binding/folding step
    • Theory + Practical
  • Thermo–kinetic narrative with experiment links (ITC/SPR)
    • consistency checks uncertainty reporting
  • Deliverables: figures, tables, README & manifest
    • PDF CSV/TSV checksums


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