Syllabus:)Models)and)Algorithms)in)Biophysics.))AS)250.302)
)
Course)description.)An#introduction#to#physical#and#mathematical#models#used#to#
represent#biological#systems#and#phenomena.#Students#will#learn#algorithms#for#
implementing#models#computationally#and#perform#basic#implementations#in#
MATLAB.#We#will#discuss#the#types#of#approximations#made#to#develop#useful#
models#of#complex#biological#systems,#and#the#comparison#of#model#predictions#
with#experiment.#
#
The#course#contains#5#major#sections:#
1) Thermodynamics#and#basic#statistical#mechanics#
2) Dynamics#of#equilibrium#and#nonIequilibrium#systems,#equations#of#motion#
and#applications#to#molecular#systems#
3) Parameter#estimation,#optimization,#and#dimensionality#reduction#for#model#
fitting#and#data#analysis.#
4) Fluid#dynamics#and#continuum#models#(partial#differential#equations)#
5) Additional#topics:#membranes,#cytoskeletal#assembly,#networks,#action#
potentials,#gene#expression.#
#
People:))
)
Prof:#Margaret#E#Johnson,#121C#Mergenthaler#Hall#
margaret.johnson@jhu.edu#
Office#Hours:#Thursdays,#11amI12#
#
TA:)Osman#Yogurtcu,#yogurtcuon@gmail.com#
#
Lectures:)#Tuesday#and#Thursdays#from#1:30I2:45PM#in#Jenkins#107.##
#
Labs:)Labs#meet#on#Mondays#from#5I6PM#in#Jenkins#122.#
#
Required)Text:#Physical#Biology#of#the#Cell.#Phillips,#Kondev,#Theriot.#
#
Additional)Reading#will#be#selected#from#the#following#texts#and#made#available#on#
blackboard:#
Understanding#Molecular#Simulation,#Frenkel#and#Smit#
Information#Theory,#Inference,#and#Learning#Algorithms,#MacKay#
Introduction#to#Modern#Statistical#Mechanics,#David#Chandler#
Physical#Models#of#Living#Systems,#Philip#Nelson#
Molecular#Modeling#and#Simulation:#An#Interdisciplinary#Guide,#Tamar#Schlick#
Numerical#Recipes#(www.nr.com)#
#
Prerequisite:)An#intro#computing#course.#Calculus.#
)
Grading:#40%#of#the#grading#will#be#based#on#biIweekly#homework#sets,#30%#will#
be#based#on#the#two#exams,#and#30%#will#be#based#on#the#final#project.##
#
Final)Project:)Global)optimization)of)on)and)offJlattice)protein)models.))
The#final#project#will#build#off#code#developed#throughout#the#homework#
assignment#to#study#two#different#coarse#grained#modeling#approaches#for#studying#
proteins#in#silico.#Students#will#be#given#target#protein#sequences#and#use#the#on#and#
offIlattice#models#of#protein#structure#and#energetics#to#sample#possible#folded#
protein#structures.##They#will#compete#to#identify#the#global#minimum#of#the#protein#
structure,#which#represents#the#native#folded#structure,#using#global#optimization#
techniques.###
The#final#project#is#evaluated#based#on#a#final#presentation#of#the#project#(during#the#
final#exam#time),#as#well#as#a#submission#of#the#code#used#and#a#brief#written#
summary#of#the#optimal#protein#structures#found.#
)
Ethics:)
From#the#undergraduate#academic#ethics#board:#“Undergraduate#students#enrolled#
in#the#Krieger#School#of#Arts#and#Sciences#or#the#Whiting#School#of#Engineering#at#
the#Johns#Hopkins#University#assume#a#duty#to#conduct#themselves#in#a#manner#
appropriate#to#the#University's#mission#as#an#institution#of#higher#learning.#Students#
are#obliged#to#refrain#from#acts#which#they#know,#or#under#circumstances#have#
reason#to#know,#violate#the#academic#integrity#of#the#University.”#
Violations#include#and#are#not#limited#to#cheating,#plagiarism,#and#submitting#work#
that#is#not#your#own,#and#will#result#in#a#zero#on#the#assignment.#
#
#
Lecture)details)below:)**Labs#meet#on#Mondays,#Except#first#day#of#classes#
)
#
#
Date)
Jan#28#
Lecture)
1#
Topic)
Introduction#to#models#and#
algorithms#
Dimensional#analysis,#
length/time#scales,#model#
development#
Probability#and#random#
numbers,#sampling#from#
distributions.#
Thermodynamics,#Ideal#Gas#
Feb#2#
2#
Feb#4#
3#
Feb#9#
4#
Feb#11#
5#
Feb#16#
6#
Feb#18#
7#
Feb#23#
8#
Feb#25#
Mar#1#
Mar#3#
9#
10#
11#
Mar#8#
Mar#10#
#
12#
Statistical#Mechanics,#microI
macroscopic#calculations#
Monte#Carlo#methods.#Lattice#
models#
ODEs,#chemical#kinetics,#and#
Gillespie#algorithm.#
Molecular#Dynamics#(MD)#and#
PDEs#
MD#&#Langevin#Dynamics#
Diffusion#and#random#walks#
Brownian#dynamics,#reaction#
dynamics,#chain#models##
Exam#1#
Parameter#estimation,#fitting#
Spring#
Break#
Mar#22#
Mar#24#
#
#
13#
14#
Mar#29#
15#
Mar#31#
16#
Apr#5#
18#
Apr#7#
Apr#12#
Apr#14#
19#
20#
21#
Apr#19#
Apr#21#
#
22#
Apr#26#
23#
Apr#28#
24#
Clustering,#classification.#
Optimization,#simulated#
annealing#
Dimensionality#reduction,#
Principal#Component#Analysis#
Hydrodynamics,#Reynolds#
number#
More#Fluid#dynamics,#NavierI
Stokes#
Solving#continuum#models#
Membrane#mechanics##
Assembly,#microtubule#
dynamics#
Exam#2#
Electricity#and#the#HodgkinI
Huxley#model#
Protein#interaction#networks#
and#network#analysis#
Gene#expression#and#feedback#
Extra)Reading))
Phys.#Biol.#Of#Cell:#Chapter#
1#
Phys.#Biol.#Of#Cell:#Chapter#
2#&3#
MacKay:#Chapter#2#
Numerical#Recipes#on#
Random#numbers#
PBoC#Chapter#5.#
ChandlerIChapter#1#
PBoC#Chapter#6.#
ChandlerIChapter#3#
Frenkel#and#Smit,#Chapter#
3#
Numerical#Methods#and#
Analysis,#Ch.#6#
Frenkel#and#Smit,#Ch.#4#(to#
section#4.4)#
Frenkel#and#Smit,#Ch.#4.##
PBoC#Ch.#13#
PBoC#Ch.#8,#16#
MacKay,#Ch.#22,#Nelson,#
Ch.#6#
#
MacKay,#Ch.#20#and#25#
Schlick,#Ch.#10#
Schlick,#Ch.#14,#section#
14.4#
PBoC#Ch.#12#
PBoC#Ch.#12#
Haberman,#Ch.#6#
PBoC#Ch.#11#
PBoC#Ch.#15,#(structure#
discussion#in#Ch.#10)#
PBoC#Ch.#17#
PBoC#Ch#19#
#
#
#