Computational methods in Biophysics

Francesca Maria Marchetti

Lecturer

Francesca Maria Marchetti

Tel. 91 497 5590
e-mail: francesca.marchetti (at) uam.es

Departamento de Física Teórica de la Materia Condensada

Timetable

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Classes are all on Fridays 9:30-12:30
Aula:
CIE7 01.17.LD.101: módulo 17, classroom 101

September

Fri 29

October

Fri 6

Fri 20

November

Fri 3

Fri 17

Fri 24

December

Fri 1

Fri 15

January

Exam: Monday 22nd of January 2018

Notes & Problem Sets

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Weekly problem sets

Week 1 problems

Week 2 problems

Week 7 problems

Week 8 problems

class examples 29/09/2017

class examples 6/10/2017

class examples 24/11/2017, Euler_1ODE.m, modifiedEuler_1ODE.m, RK2ndO_1ODE.m

class examples 01/12/2017,
RK2ndO_1ODE.m, RK2ndO_2ODE.m

class examples 15/12/2017, RK2ndO_cpld1DE.m, ind_int_trpz.m

Exam (22/01/2018)

solution

Notes & problem solutions

Part 1

Notes on Part 1
Basic concepts Matlab as a calculator Variables Vectors & matrices Vectors & matrix operations Commands defining vectors: ':' & 'linspace'	solutions
Scripts & plotting Scripts 'plot'	solutions
Numerical derivation & integration numerical derivation first and second order approximations numerical integration Applications: position, velocity and acceleration	solutions

Anonymous functions
Use of external function routines derivation integration	example_derivative.m diff_first.m	derivative_point.m indef_integral.m indef_integral_sp.m
Conditions and loops loop 'for' Command 'if' loop 'while'		solutions
Advanced plotting Plotting scalar fields Plotting vector fields

Part 2

Notes on Part 2
System of linear equations inverse matrix	solutions
Roots of a function bisection method Newton--Raphson method energy conservation	solutions
Use of external function rutines: roots of a function	example-use-external-functions.m bisection.m NewtonRaphson.m NewtonRaphson_noanalytic.m

Differential equations Ordinary differential equations (ODEs) First order ODEs: Euler method Second order ODEs: Euler method	solutions Euler_method.m second_ord_Euler.m
modified Euler method second order Runge-Kutta method	solutions RK_method.m modEuler_method.m
Harmonic oscillator simple damped driven (resonance) Planar pendulum phase space diagram	harmonic-oscillator.m planar-pendulum.m RK_pendulo.m
Critical points and phase lines first order ODE coupled ODEs	solutions RK_1ODE.m
Applications Logistic equation Pray and predators	logistic.m predator-prey.m RK_pray_pred.m RK_2coupledODE.m

Data analysis descriptive statistics probability distributions	quant_statistics.m probability_distr.m
data fitting	data_fitting.m

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