├── .DS_Store ├── .github └── workflows │ └── deploy.yml ├── .ipynb_checkpoints ├── _toc-checkpoint.yml └── index-checkpoint.md ├── .nvimlog ├── 1_stats ├── Diffusion.ipynb ├── Entropy.ipynb ├── Probabilities_Counting.ipynb ├── RW_theory.md ├── Random_Variables.ipynb ├── figs │ ├── 1d_random_walk.gif │ ├── 2d_gas_simulation.gif │ ├── CK-visual.png │ ├── RV.png │ ├── bayes.png │ ├── dp_diffusion.png │ ├── flux1d.png │ ├── flux2d.png │ ├── history_diff.png │ └── max-dem.png └── intro.md ├── 2_thermo ├── .ipynb_checkpoints │ ├── 01_Thermo-checkpoint.ipynb │ └── 02_Legendre-checkpoint.ipynb ├── 01_Thermo.ipynb ├── 02_FreeEnergies.ipynb ├── figs │ ├── .ipynb_checkpoints │ │ └── adiabat-checkpoint.png │ ├── Adiabats.png │ ├── Leg1.png │ ├── Legendre.png │ ├── NO1.png │ ├── NO2.png │ ├── adiabat.png │ ├── concave_convex.png │ ├── part1.png │ ├── plank.png │ ├── polymer.png │ └── recurrence.jpg └── intro.md ├── 3_ensembles ├── .ipynb_checkpoints │ ├── Ensembles-checkpoint.ipynb │ ├── ensemble_overview-checkpoint.md │ ├── intro-checkpoint.md │ ├── npt-checkpoint.ipynb │ ├── nve-checkpoint.ipynb │ ├── nvt-checkpoint.ipynb │ └── phase_space-checkpoint.ipynb ├── ensemble_overview.md ├── figs │ ├── 1d-pspace.png │ ├── Black_body_rad.jpg │ ├── adsorption.png │ ├── bottleocean.jpg │ ├── energy-rugged.png │ ├── ensembl.png │ ├── folding.png │ ├── harmonic.png │ ├── liuville.png │ ├── pib-states.png │ └── spin-states.png ├── intro.md ├── npt.ipynb ├── nve.ipynb ├── nvt.ipynb ├── phase_space.ipynb ├── photons_phonons.ipynb ├── quantum_systems.ipynb └── random.md ├── 4_ising ├── 00_phase_tranistions.ipynb ├── 01_MC.ipynb ├── 02_MCMC.ipynb ├── 03_MF.ipynb ├── 03_MeanField.ipynb ├── figs │ ├── 1st_2nd_Ising (1).png │ ├── Curie.png │ ├── arrows-ising.png │ ├── crit1.png │ ├── crit2.png │ ├── crit3.png │ ├── crit4.png │ ├── critical-ising.png │ ├── first_sec_ps.png │ ├── fluid-analogy.png │ ├── gas-universality.png │ ├── phase-diagram.png │ ├── spont-mag.png │ ├── umbrealla-2.png │ ├── umbrella-1.png │ └── universality-ising.png └── intro.md ├── 5_fluids ├── Intro2Fluids.ipynb ├── Intro2MD.ipynb ├── figs │ ├── 1466565515216.jpg │ ├── g2_2.png │ ├── gr1_1.png │ ├── gr3_3.png │ ├── gr4_4.png │ ├── mcmd.png │ ├── md-time.png │ ├── md-timescales.png │ ├── pbc1.png │ └── pbc2.png ├── intro.md ├── langevin.ipynb ├── md_lj.ipynb ├── pbc_fig1.gif ├── pbc_fig2.gif └── vdw.ipynb ├── 6_kinetics └── intro.md ├── README.md ├── _config.yml ├── _toc.yml ├── index.md ├── index_fig.jpg ├── labs ├── finals │ ├── glauber.ipynb │ ├── intro.md │ ├── lj_ab_monomer.ipynb │ ├── lj_ab_polymer.ipynb │ ├── nucleation.ipynb │ └── tst.ipynb ├── lab2 │ └── intro.md ├── lab4 │ ├── .ipynb_checkpoints │ │ ├── TwoState-checkpoint.ipynb │ │ ├── intro-checkpoint.md │ │ ├── mass_action-checkpoint.ipynb │ │ └── nvt_application-checkpoint.ipynb │ ├── TwoState.ipynb │ ├── intro.md │ ├── mass_action.ipynb │ └── nvt_application.ipynb ├── lab5 │ ├── Wolf.ipynb │ ├── enhance-sampling.ipynb │ ├── intro.md │ ├── markov_chains.ipynb │ ├── parallel_temp_ising2D.py │ └── vdw_autodgrad.ipynb ├── lab6 │ ├── .ipynb_checkpoints │ │ ├── intro-checkpoint.md │ │ ├── openmm_double_well-checkpoint.ipynb │ │ ├── openmm_ethane-checkpoint.ipynb │ │ └── openmm_lj_chain-checkpoint.ipynb │ ├── alanine_dipeptide.ipynb │ ├── intro.md │ ├── lj_melt.ipynb │ ├── openmm_double_well.ipynb │ ├── openmm_ethane.ipynb │ ├── openmm_harm_osc.ipynb │ ├── openmm_lj_chain.ipynb │ ├── openmm_villin.ipynb │ └── water_box_sim.ipynb ├── maxwell-demon │ ├── code │ │ └── maxwells_demon.py │ ├── figs │ │ ├── LandauerExperiment.png │ │ └── LandauerExperiment2.jpg │ ├── intro.md │ └── landauer.ipynb ├── np-lab │ ├── 1d_gas_sim.ipynb │ ├── 2d_gas_sim.ipynb │ ├── intro.md │ ├── linear_functions.ipynb │ ├── np_prob.ipynb │ └── sinc_function.ipynb ├── py-lab │ ├── figs │ │ ├── aggregate-numpy.png │ │ ├── list.png │ │ ├── list_slice.png │ │ ├── markov-chain.png │ │ ├── mc_casino.jpg │ │ ├── numpy-matrix-broadcast.png │ │ ├── numpy-matrix-indexing.png │ │ ├── numpy1.png │ │ ├── numpy2.png │ │ ├── numpy_3d.png │ │ ├── numpy_index.png │ │ ├── py-popular.png │ │ ├── py-popular2.png │ │ ├── python-data-types.jpeg │ │ ├── sliceList.jpg │ │ └── whyPy.png │ ├── intro.md │ ├── intro2numpy.ipynb │ ├── intro2py.ipynb │ ├── intro2viz.ipynb │ └── python_OOP_challenge.ipynb └── rw-lab │ ├── .ipynb_checkpoints │ ├── intro-checkpoint.md │ └── polymer-conf-checkpoint.ipynb │ ├── InverseTransform.ipynb │ ├── change_rv_jax.ipynb │ ├── intro.md │ ├── langevin.ipynb │ ├── polymer-conf.ipynb │ └── rw_lab.ipynb ├── logo.jpg ├── references.bib ├── requirements.txt └── schedule.md /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/.DS_Store -------------------------------------------------------------------------------- /.github/workflows/deploy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/.github/workflows/deploy.yml -------------------------------------------------------------------------------- /.ipynb_checkpoints/_toc-checkpoint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/.ipynb_checkpoints/_toc-checkpoint.yml -------------------------------------------------------------------------------- /.ipynb_checkpoints/index-checkpoint.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/.ipynb_checkpoints/index-checkpoint.md -------------------------------------------------------------------------------- /.nvimlog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/.nvimlog -------------------------------------------------------------------------------- /1_stats/Diffusion.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/Diffusion.ipynb -------------------------------------------------------------------------------- /1_stats/Entropy.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/Entropy.ipynb -------------------------------------------------------------------------------- /1_stats/Probabilities_Counting.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/Probabilities_Counting.ipynb -------------------------------------------------------------------------------- /1_stats/RW_theory.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/RW_theory.md -------------------------------------------------------------------------------- /1_stats/Random_Variables.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/Random_Variables.ipynb -------------------------------------------------------------------------------- /1_stats/figs/1d_random_walk.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/1d_random_walk.gif -------------------------------------------------------------------------------- /1_stats/figs/2d_gas_simulation.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/2d_gas_simulation.gif -------------------------------------------------------------------------------- /1_stats/figs/CK-visual.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/CK-visual.png -------------------------------------------------------------------------------- /1_stats/figs/RV.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/RV.png -------------------------------------------------------------------------------- /1_stats/figs/bayes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/bayes.png -------------------------------------------------------------------------------- /1_stats/figs/dp_diffusion.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/dp_diffusion.png -------------------------------------------------------------------------------- /1_stats/figs/flux1d.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/flux1d.png -------------------------------------------------------------------------------- /1_stats/figs/flux2d.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/flux2d.png -------------------------------------------------------------------------------- /1_stats/figs/history_diff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/history_diff.png -------------------------------------------------------------------------------- /1_stats/figs/max-dem.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/figs/max-dem.png -------------------------------------------------------------------------------- /1_stats/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/1_stats/intro.md -------------------------------------------------------------------------------- /2_thermo/.ipynb_checkpoints/01_Thermo-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/.ipynb_checkpoints/01_Thermo-checkpoint.ipynb -------------------------------------------------------------------------------- /2_thermo/.ipynb_checkpoints/02_Legendre-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/.ipynb_checkpoints/02_Legendre-checkpoint.ipynb -------------------------------------------------------------------------------- /2_thermo/01_Thermo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/01_Thermo.ipynb -------------------------------------------------------------------------------- /2_thermo/02_FreeEnergies.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/02_FreeEnergies.ipynb -------------------------------------------------------------------------------- /2_thermo/figs/.ipynb_checkpoints/adiabat-checkpoint.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/.ipynb_checkpoints/adiabat-checkpoint.png -------------------------------------------------------------------------------- /2_thermo/figs/Adiabats.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/Adiabats.png -------------------------------------------------------------------------------- /2_thermo/figs/Leg1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/Leg1.png -------------------------------------------------------------------------------- /2_thermo/figs/Legendre.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/Legendre.png -------------------------------------------------------------------------------- /2_thermo/figs/NO1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/NO1.png -------------------------------------------------------------------------------- /2_thermo/figs/NO2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/NO2.png -------------------------------------------------------------------------------- /2_thermo/figs/adiabat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/adiabat.png -------------------------------------------------------------------------------- /2_thermo/figs/concave_convex.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/concave_convex.png -------------------------------------------------------------------------------- /2_thermo/figs/part1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/part1.png -------------------------------------------------------------------------------- /2_thermo/figs/plank.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/plank.png -------------------------------------------------------------------------------- /2_thermo/figs/polymer.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/polymer.png -------------------------------------------------------------------------------- /2_thermo/figs/recurrence.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/figs/recurrence.jpg -------------------------------------------------------------------------------- /2_thermo/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/2_thermo/intro.md -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/Ensembles-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/Ensembles-checkpoint.ipynb -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/ensemble_overview-checkpoint.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/ensemble_overview-checkpoint.md -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/intro-checkpoint.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/intro-checkpoint.md -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/npt-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/npt-checkpoint.ipynb -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/nve-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/nve-checkpoint.ipynb -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/nvt-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/nvt-checkpoint.ipynb -------------------------------------------------------------------------------- /3_ensembles/.ipynb_checkpoints/phase_space-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/.ipynb_checkpoints/phase_space-checkpoint.ipynb -------------------------------------------------------------------------------- /3_ensembles/ensemble_overview.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/ensemble_overview.md -------------------------------------------------------------------------------- /3_ensembles/figs/1d-pspace.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/1d-pspace.png -------------------------------------------------------------------------------- /3_ensembles/figs/Black_body_rad.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/Black_body_rad.jpg -------------------------------------------------------------------------------- /3_ensembles/figs/adsorption.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/adsorption.png -------------------------------------------------------------------------------- /3_ensembles/figs/bottleocean.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/bottleocean.jpg -------------------------------------------------------------------------------- /3_ensembles/figs/energy-rugged.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/energy-rugged.png -------------------------------------------------------------------------------- /3_ensembles/figs/ensembl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/ensembl.png -------------------------------------------------------------------------------- /3_ensembles/figs/folding.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/folding.png -------------------------------------------------------------------------------- /3_ensembles/figs/harmonic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/harmonic.png -------------------------------------------------------------------------------- /3_ensembles/figs/liuville.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/liuville.png -------------------------------------------------------------------------------- /3_ensembles/figs/pib-states.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/pib-states.png -------------------------------------------------------------------------------- /3_ensembles/figs/spin-states.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/figs/spin-states.png -------------------------------------------------------------------------------- /3_ensembles/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/intro.md -------------------------------------------------------------------------------- /3_ensembles/npt.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/npt.ipynb -------------------------------------------------------------------------------- /3_ensembles/nve.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/nve.ipynb -------------------------------------------------------------------------------- /3_ensembles/nvt.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/nvt.ipynb -------------------------------------------------------------------------------- /3_ensembles/phase_space.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/phase_space.ipynb -------------------------------------------------------------------------------- /3_ensembles/photons_phonons.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/photons_phonons.ipynb -------------------------------------------------------------------------------- /3_ensembles/quantum_systems.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/quantum_systems.ipynb -------------------------------------------------------------------------------- /3_ensembles/random.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/3_ensembles/random.md -------------------------------------------------------------------------------- /4_ising/00_phase_tranistions.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/00_phase_tranistions.ipynb -------------------------------------------------------------------------------- /4_ising/01_MC.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/01_MC.ipynb -------------------------------------------------------------------------------- /4_ising/02_MCMC.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/02_MCMC.ipynb -------------------------------------------------------------------------------- /4_ising/03_MF.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/03_MF.ipynb -------------------------------------------------------------------------------- /4_ising/03_MeanField.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/03_MeanField.ipynb -------------------------------------------------------------------------------- /4_ising/figs/1st_2nd_Ising (1).png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/1st_2nd_Ising (1).png -------------------------------------------------------------------------------- /4_ising/figs/Curie.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/Curie.png -------------------------------------------------------------------------------- /4_ising/figs/arrows-ising.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/arrows-ising.png -------------------------------------------------------------------------------- /4_ising/figs/crit1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/crit1.png -------------------------------------------------------------------------------- /4_ising/figs/crit2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/crit2.png -------------------------------------------------------------------------------- /4_ising/figs/crit3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/crit3.png -------------------------------------------------------------------------------- /4_ising/figs/crit4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/crit4.png -------------------------------------------------------------------------------- /4_ising/figs/critical-ising.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/critical-ising.png -------------------------------------------------------------------------------- /4_ising/figs/first_sec_ps.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/first_sec_ps.png -------------------------------------------------------------------------------- /4_ising/figs/fluid-analogy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/fluid-analogy.png -------------------------------------------------------------------------------- /4_ising/figs/gas-universality.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/gas-universality.png -------------------------------------------------------------------------------- /4_ising/figs/phase-diagram.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/phase-diagram.png -------------------------------------------------------------------------------- /4_ising/figs/spont-mag.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/spont-mag.png -------------------------------------------------------------------------------- /4_ising/figs/umbrealla-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/umbrealla-2.png -------------------------------------------------------------------------------- /4_ising/figs/umbrella-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/umbrella-1.png -------------------------------------------------------------------------------- /4_ising/figs/universality-ising.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/figs/universality-ising.png -------------------------------------------------------------------------------- /4_ising/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/4_ising/intro.md -------------------------------------------------------------------------------- /5_fluids/Intro2Fluids.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/Intro2Fluids.ipynb -------------------------------------------------------------------------------- /5_fluids/Intro2MD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/Intro2MD.ipynb -------------------------------------------------------------------------------- /5_fluids/figs/1466565515216.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/1466565515216.jpg -------------------------------------------------------------------------------- /5_fluids/figs/g2_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/g2_2.png -------------------------------------------------------------------------------- /5_fluids/figs/gr1_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/gr1_1.png -------------------------------------------------------------------------------- /5_fluids/figs/gr3_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/gr3_3.png -------------------------------------------------------------------------------- /5_fluids/figs/gr4_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/gr4_4.png -------------------------------------------------------------------------------- /5_fluids/figs/mcmd.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/mcmd.png -------------------------------------------------------------------------------- /5_fluids/figs/md-time.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/md-time.png -------------------------------------------------------------------------------- /5_fluids/figs/md-timescales.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/md-timescales.png -------------------------------------------------------------------------------- /5_fluids/figs/pbc1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/pbc1.png -------------------------------------------------------------------------------- /5_fluids/figs/pbc2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/figs/pbc2.png -------------------------------------------------------------------------------- /5_fluids/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/intro.md -------------------------------------------------------------------------------- /5_fluids/langevin.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/langevin.ipynb -------------------------------------------------------------------------------- /5_fluids/md_lj.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/md_lj.ipynb -------------------------------------------------------------------------------- /5_fluids/pbc_fig1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/pbc_fig1.gif -------------------------------------------------------------------------------- /5_fluids/pbc_fig2.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/pbc_fig2.gif -------------------------------------------------------------------------------- /5_fluids/vdw.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/5_fluids/vdw.ipynb -------------------------------------------------------------------------------- /6_kinetics/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/6_kinetics/intro.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/_config.yml -------------------------------------------------------------------------------- /_toc.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/_toc.yml -------------------------------------------------------------------------------- /index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/index.md -------------------------------------------------------------------------------- /index_fig.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/index_fig.jpg -------------------------------------------------------------------------------- /labs/finals/glauber.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/finals/glauber.ipynb -------------------------------------------------------------------------------- /labs/finals/intro.md: -------------------------------------------------------------------------------- 1 | # Final Projects -------------------------------------------------------------------------------- /labs/finals/lj_ab_monomer.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/finals/lj_ab_monomer.ipynb -------------------------------------------------------------------------------- /labs/finals/lj_ab_polymer.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/finals/lj_ab_polymer.ipynb -------------------------------------------------------------------------------- /labs/finals/nucleation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/finals/nucleation.ipynb -------------------------------------------------------------------------------- /labs/finals/tst.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/finals/tst.ipynb -------------------------------------------------------------------------------- /labs/lab2/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab2/intro.md -------------------------------------------------------------------------------- /labs/lab4/.ipynb_checkpoints/TwoState-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab4/.ipynb_checkpoints/TwoState-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/lab4/.ipynb_checkpoints/intro-checkpoint.md: -------------------------------------------------------------------------------- 1 | # Application of ensembles -------------------------------------------------------------------------------- /labs/lab4/.ipynb_checkpoints/mass_action-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab4/.ipynb_checkpoints/mass_action-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/lab4/.ipynb_checkpoints/nvt_application-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab4/.ipynb_checkpoints/nvt_application-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/lab4/TwoState.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab4/TwoState.ipynb -------------------------------------------------------------------------------- /labs/lab4/intro.md: -------------------------------------------------------------------------------- 1 | # Application of ensembles -------------------------------------------------------------------------------- /labs/lab4/mass_action.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab4/mass_action.ipynb -------------------------------------------------------------------------------- /labs/lab4/nvt_application.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab4/nvt_application.ipynb -------------------------------------------------------------------------------- /labs/lab5/Wolf.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab5/Wolf.ipynb -------------------------------------------------------------------------------- /labs/lab5/enhance-sampling.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab5/enhance-sampling.ipynb -------------------------------------------------------------------------------- /labs/lab5/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab5/intro.md -------------------------------------------------------------------------------- /labs/lab5/markov_chains.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab5/markov_chains.ipynb -------------------------------------------------------------------------------- /labs/lab5/parallel_temp_ising2D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab5/parallel_temp_ising2D.py -------------------------------------------------------------------------------- /labs/lab5/vdw_autodgrad.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab5/vdw_autodgrad.ipynb -------------------------------------------------------------------------------- /labs/lab6/.ipynb_checkpoints/intro-checkpoint.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /labs/lab6/.ipynb_checkpoints/openmm_double_well-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/.ipynb_checkpoints/openmm_double_well-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/lab6/.ipynb_checkpoints/openmm_ethane-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/.ipynb_checkpoints/openmm_ethane-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/lab6/.ipynb_checkpoints/openmm_lj_chain-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/.ipynb_checkpoints/openmm_lj_chain-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/lab6/alanine_dipeptide.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/alanine_dipeptide.ipynb -------------------------------------------------------------------------------- /labs/lab6/intro.md: -------------------------------------------------------------------------------- 1 | # Simulating Fluids -------------------------------------------------------------------------------- /labs/lab6/lj_melt.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/lj_melt.ipynb -------------------------------------------------------------------------------- /labs/lab6/openmm_double_well.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/openmm_double_well.ipynb -------------------------------------------------------------------------------- /labs/lab6/openmm_ethane.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/openmm_ethane.ipynb -------------------------------------------------------------------------------- /labs/lab6/openmm_harm_osc.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/openmm_harm_osc.ipynb -------------------------------------------------------------------------------- /labs/lab6/openmm_lj_chain.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/openmm_lj_chain.ipynb -------------------------------------------------------------------------------- /labs/lab6/openmm_villin.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/openmm_villin.ipynb -------------------------------------------------------------------------------- /labs/lab6/water_box_sim.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/lab6/water_box_sim.ipynb -------------------------------------------------------------------------------- /labs/maxwell-demon/code/maxwells_demon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/maxwell-demon/code/maxwells_demon.py -------------------------------------------------------------------------------- /labs/maxwell-demon/figs/LandauerExperiment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/maxwell-demon/figs/LandauerExperiment.png -------------------------------------------------------------------------------- /labs/maxwell-demon/figs/LandauerExperiment2.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/maxwell-demon/figs/LandauerExperiment2.jpg -------------------------------------------------------------------------------- /labs/maxwell-demon/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/maxwell-demon/intro.md -------------------------------------------------------------------------------- /labs/maxwell-demon/landauer.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/maxwell-demon/landauer.ipynb -------------------------------------------------------------------------------- /labs/np-lab/1d_gas_sim.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/np-lab/1d_gas_sim.ipynb -------------------------------------------------------------------------------- /labs/np-lab/2d_gas_sim.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/np-lab/2d_gas_sim.ipynb -------------------------------------------------------------------------------- /labs/np-lab/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/np-lab/intro.md -------------------------------------------------------------------------------- /labs/np-lab/linear_functions.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/np-lab/linear_functions.ipynb -------------------------------------------------------------------------------- /labs/np-lab/np_prob.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/np-lab/np_prob.ipynb -------------------------------------------------------------------------------- /labs/np-lab/sinc_function.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/np-lab/sinc_function.ipynb -------------------------------------------------------------------------------- /labs/py-lab/figs/aggregate-numpy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/aggregate-numpy.png -------------------------------------------------------------------------------- /labs/py-lab/figs/list.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/list.png -------------------------------------------------------------------------------- /labs/py-lab/figs/list_slice.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/list_slice.png -------------------------------------------------------------------------------- /labs/py-lab/figs/markov-chain.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/markov-chain.png -------------------------------------------------------------------------------- /labs/py-lab/figs/mc_casino.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/mc_casino.jpg -------------------------------------------------------------------------------- /labs/py-lab/figs/numpy-matrix-broadcast.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/numpy-matrix-broadcast.png -------------------------------------------------------------------------------- /labs/py-lab/figs/numpy-matrix-indexing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/numpy-matrix-indexing.png -------------------------------------------------------------------------------- /labs/py-lab/figs/numpy1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/numpy1.png -------------------------------------------------------------------------------- /labs/py-lab/figs/numpy2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/numpy2.png -------------------------------------------------------------------------------- /labs/py-lab/figs/numpy_3d.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/numpy_3d.png -------------------------------------------------------------------------------- /labs/py-lab/figs/numpy_index.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/numpy_index.png -------------------------------------------------------------------------------- /labs/py-lab/figs/py-popular.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/py-popular.png -------------------------------------------------------------------------------- /labs/py-lab/figs/py-popular2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/py-popular2.png -------------------------------------------------------------------------------- /labs/py-lab/figs/python-data-types.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/python-data-types.jpeg -------------------------------------------------------------------------------- /labs/py-lab/figs/sliceList.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/sliceList.jpg -------------------------------------------------------------------------------- /labs/py-lab/figs/whyPy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/figs/whyPy.png -------------------------------------------------------------------------------- /labs/py-lab/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/intro.md -------------------------------------------------------------------------------- /labs/py-lab/intro2numpy.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/intro2numpy.ipynb -------------------------------------------------------------------------------- /labs/py-lab/intro2py.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/intro2py.ipynb -------------------------------------------------------------------------------- /labs/py-lab/intro2viz.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/intro2viz.ipynb -------------------------------------------------------------------------------- /labs/py-lab/python_OOP_challenge.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/py-lab/python_OOP_challenge.ipynb -------------------------------------------------------------------------------- /labs/rw-lab/.ipynb_checkpoints/intro-checkpoint.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/.ipynb_checkpoints/intro-checkpoint.md -------------------------------------------------------------------------------- /labs/rw-lab/.ipynb_checkpoints/polymer-conf-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/.ipynb_checkpoints/polymer-conf-checkpoint.ipynb -------------------------------------------------------------------------------- /labs/rw-lab/InverseTransform.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/InverseTransform.ipynb -------------------------------------------------------------------------------- /labs/rw-lab/change_rv_jax.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/change_rv_jax.ipynb -------------------------------------------------------------------------------- /labs/rw-lab/intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/intro.md -------------------------------------------------------------------------------- /labs/rw-lab/langevin.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/langevin.ipynb -------------------------------------------------------------------------------- /labs/rw-lab/polymer-conf.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/polymer-conf.ipynb -------------------------------------------------------------------------------- /labs/rw-lab/rw_lab.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/labs/rw-lab/rw_lab.ipynb -------------------------------------------------------------------------------- /logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/logo.jpg -------------------------------------------------------------------------------- /references.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/references.bib -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/requirements.txt -------------------------------------------------------------------------------- /schedule.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DPotoyan/Statmech4ChemBio/HEAD/schedule.md --------------------------------------------------------------------------------