Birmingham , The Summit
Huntsville , Bridge Street
Anchorage , Anchorage 5th Avenue Mall
Chandler , Chandler Fashion Center
Gilbert , SanTan Village
Glendale , Arrowhead
Scottsdale , Scottsdale Fashion Square
Scottsdale , Scottsdale Quarter
Tucson , La Encantada
Little Rock , The Promenade at Chenal
Bakersfield , Valley Plaza
Berkeley , 4th Street
Brea , Brea Mall
Burlingame , Burlingame
Canoga Park , Topanga
Carlsbad , Carlsbad
Cerritos , Los Cerritos
Chula Vista , Otay Ranch
Corte Madera , Corte Madera
Costa Mesa , South Coast Plaza
Cupertino , Infinite Loop
Cupertino , Apple Park Visitor Center
Emeryville , Bay Street
Escondido , North County
Fresno , Fashion Fair
Glendale , Glendale Galleria
Glendale , The Americana at Brand
Irvine , Irvine Spectrum Center
Los Angeles , The Grove
Los Angeles , Tower Theatre
Los Angeles , Beverly Center
Los Angeles , Century City
Los Gatos , Los Gatos
Manhattan Beach , Manhattan Village
Mission Viejo , Mission Viejo
Modesto , Vintage Faire
Monterey , Del Monte
Newport Beach , Fashion Island
Northridge , Northridge
Palm Desert , El Paseo Village
Palo Alto , Stanford Shopping Center
Palo Alto , Palo Alto
Pasadena , Pasadena
Pleasanton , Stoneridge Mall
Rancho Cucamonga , Victoria Gardens
Roseville , Roseville
Sacramento , Arden Fair
San Diego , UTC
San Diego , Fashion Valley
San Francisco , Chestnut Street
San Francisco , Stonestown
San Francisco , Union Square
San Jose , Oakridge
San Luis Obispo , Higuera Street
San Mateo , Hillsdale
Santa Barbara , State Street
Santa Clara , Valley Fair
Santa Monica , Third Street Promenade
Santa Rosa , Santa Rosa Plaza
Sherman Oaks , Sherman Oaks
Temecula , Promenade Temecula
Thousand Oaks , The Oaks
Valencia , Valencia Town Center
Walnut Creek , Broadway Plaza
Boulder , Twenty Ninth Street
Broomfield , FlatIron Crossing
Colorado Springs , The Promenade Shops at Briargate
Denver , Cherry Creek
Littleton , Aspen Grove
Lone Tree , Park Meadows
Danbury , Danbury Fair Mall
Farmington , Westfarms
Greenwich , Greenwich Avenue
New Haven , New Haven
Norwalk , SoNo Collection
South Windsor , Evergreen Walk
Trumbull , Trumbull
Newark , Christiana Mall
Washington , Carnegie Library
Washington , Georgetown
Altamonte Springs , Altamonte
Aventura , Aventura
Boca Raton , Boca Raton
Brandon , Brandon
Estero , Coconut Point
Fort Lauderdale , The Galleria
Jacksonville , St. Johns Town Center
Miami , Dadeland
Miami , Brickell City Centre
Miami , The Falls
Miami Beach , Lincoln Road
Naples , Waterside Shops
Orlando , Millenia
Orlando , Florida Mall
Palm Beach Gardens , The Gardens Mall
Sarasota , University Town Center
Tampa , International Plaza
Wellington , Wellington Green
Alpharetta , Avalon
Atlanta , Perimeter
Atlanta , Lenox Square
Atlanta , Cumberland Mall
Augusta , Augusta
Buford , Mall of Georgia
Boise , Boise Towne Square
Chicago , Lincoln Park
Chicago , Michigan Avenue
Deer Park , Deer Park
Naperville , Main Place
Northbrook , Northbrook
Oak Brook , Oakbrook
Orland Park , Orland Square Mall
Schaumburg , Woodfield
Skokie , Old Orchard
Indianapolis , The Fashion Mall at Keystone
Mishawaka , University Park Mall
West Des Moines , Jordan Creek
Leawood , Leawood
Lexington , Fritz Farm
Louisville , Oxmoor
Baton Rouge , Mall of Louisiana
Metairie , Lakeside Shopping Center
South Portland , Maine Mall
Annapolis , Annapolis
Bethesda , Bethesda Row
Bethesda , Montgomery Mall
Columbia , Columbia
Towson , Towson Town Center
Boston , Boylston Street
Braintree , South Shore
Burlington , Burlington
Cambridge , CambridgeSide
Chestnut Hill , Chestnut Hill
Dedham , Legacy Place
Hingham , Derby Street
Holyoke , Holyoke
Lynnfield , MarketStreet
Marlborough , Solomon Pond Mall
Natick , Natick
Ann Arbor , Briarwood
Clinton Township , Partridge Creek
Grand Rapids , Woodland
Lansing , Eastwood Towne Center
Novi , Twelve Oaks
Troy , Somerset
Ridgeland , Renaissance at Colony Park
Omaha , Village Pointe
Las Vegas , Summerlin
Las Vegas , The Forum Shops
Las Vegas , Fashion Show
Las Vegas , Town Square
Reno , Summit Sierra
Bridgewater , Bridgewater
Cherry Hill , Cherry Hill
Edison , Menlo Park
Freehold , Freehold Raceway Mall
Lawrence Township , Quaker Bridge
Marlton , Sagemore
Paramus , Garden State Plaza
Rockaway , Rockaway
Short Hills , Short Hills
Wayne , Willowbrook
Woodcliff Lake , Tice's Corner
Albuquerque , ABQ Uptown
Albany , Crossgates
Brooklyn , Williamsburg
Brooklyn , Downtown Brooklyn
Buffalo , Walden Galleria
Elmhurst , Queens Center
Garden City , Roosevelt Field
Huntington Station , Walt Whitman
Lake Grove , Smith Haven
Manhasset , Manhasset
Nanuet , Nanuet
New York , Upper West Side
New York , Upper East Side
New York , SoHo
New York , Fifth Avenue
New York , World Trade Center
New York , West 14th Street
New York , Grand Central
Staten Island , Staten Island
Syracuse , Syracuse
Victor , Eastview
White Plains , The Westchester
Yonkers , Ridge Hill
Charlotte , Northlake Mall
Charlotte , SouthPark
Durham , Southpoint
Greensboro , Friendly Center
Raleigh , Crabtree Valley Mall
Akron , Summit Mall
Beavercreek , The Greene
Cincinnati , Kenwood Towne Centre
Columbus , Easton Town Center
Columbus , Polaris Fashion Place
Toledo , Franklin Park Mall
Westlake , Crocker Park
Woodmere , Eton
Oklahoma City , Penn Square
Tulsa , Woodland Hills
Ardmore , Suburban Square
King of Prussia , King of Prussia
Lancaster , Park City
Philadelphia , Walnut Street
Pittsburgh , South Hills Village
Pittsburgh , Ross Park
Pittsburgh , Shadyside
Whitehall , Lehigh Valley
Willow Grove , Willow Grove Park
Providence , Providence Place
Charleston , Charleston
Greenville , Haywood Mall
Franklin , CoolSprings Galleria
Germantown , Saddle Creek
Knoxville , West Town Mall
Nashville , Downtown Nashville
Nashville , Green Hills
Austin , Domain NORTHSIDE
Austin , Barton Creek
Dallas , Knox Street
Dallas , NorthPark Center
Dallas , Galleria Dallas
El Paso , Cielo Vista Mall
Fort Worth , University Park Village
Friendswood , Baybrook
Houston , Houston Galleria
Houston , Willowbrook Mall
Houston , Memorial City
Houston , Highland Village
San Antonio , La Cantera
San Antonio , North Star
Southlake , Southlake Town Square
Sugar Land , First Colony Mall
The Woodlands , The Woodlands
Arlington , Clarendon
Arlington , Pentagon City
Fairfax , Fair Oaks
McLean , Tysons Corner
Reston , Reston
Richmond , Short Pump Town Center
Virginia Beach , Lynnhaven Mall
Woodbridge , Potomac Town Center
Bellevue , Bellevue Square
Lynnwood , Alderwood
Seattle , University Village
Spokane , River Park Square
Tacoma , Tacoma Mall
Tukwila , Southcenter


Home
Trees
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Identifier Index
[
A
B
C
D
E
F
G
H
I
J K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
_
]
A
add_extras()
(in
cosmolopy.parameters
)
age_Gyr()
(in
AgeSpacedRedshift
)
amu_g
(in
cosmolopy.constants
)
age()
(in
cosmolopy.distance
)
AgeSpacedRedshift
(in
cosmolopy.utils
)
angstrom_cm
(in
cosmolopy.constants
)
age_flat()
(in
cosmolopy.distance
)
alpha_B_cm_s_1e4
(in
cosmolopy.constants
)
angular_diameter_distance()
(in
cosmolopy.distance
)
B
B2007_z4
(in
cosmolopy.luminosityfunction
)
B2007_z7
(in
cosmolopy.luminosityfunction
)
B2008_linear_z5
(in
cosmolopy.luminosityfunction
)
B2007_z5
(in
cosmolopy.luminosityfunction
)
B2008
(in
cosmolopy.luminosityfunction
)
baryon_densities()
(in
cosmolopy.density
)
B2007_z6
(in
cosmolopy.luminosityfunction
)
B2008_fixed
(in
cosmolopy.luminosityfunction
)
BrokenPowerlawSED
(in
cosmolopy.luminosityfunction
)
C
c_light_cm_s
(in
cosmolopy.constants
)
clumping_factor_Chary()
(in
cosmolopy.reionization
)
comoving_integrand()
(in
cosmolopy.distance
)
c_light_Mpc_Gyr
(in
cosmolopy.constants
)
clumping_factor_HB()
(in
cosmolopy.reionization
)
comoving_volume()
(in
cosmolopy.distance
)
c_light_Mpc_s
(in
cosmolopy.constants
)
collapse_fraction()
(in
cosmolopy.perturbation
)
constants
(in
cosmolopy
)
ccumulate()
(in
cosmolopy.utils
)
comoving_distance()
(in
cosmolopy.distance
)
cosmo_densities()
(in
cosmolopy.density
)
clumping_factor_BKP()
(in
cosmolopy.reionization
)
comoving_distance_transverse()
(in
cosmolopy.distance
)
cosmolopy
D
delta_lambda_delta_dl()
(in
cosmolopy.reionization
)
distance
(in
cosmolopy
)
dumb_pickle_filter()
(in
Saveable
)
density
(in
cosmolopy
)
distance_modulus()
(in
cosmolopy.magnitudes
)
diff_comoving_volume()
(in
cosmolopy.distance
)
doc
(in
cosmolopy.constants
)
E
e_z()
(in
cosmolopy.distance
)
extrap_string()
(in
Extrapolate1d
)
EH
(in
cosmolopy
)
Extrapolate1d
(in
cosmolopy.utils
)
F
f_nu_from_magAB()
(in
cosmolopy.magnitudes
)
fgrowth()
(in
cosmolopy.perturbation
)
f_nu_lambda()
(in
cosmolopy.magnitudes
)
fidcosmo
(in
cosmolopy
)
G
G_const_Mpc_Msun_s
(in
cosmolopy.constants
)
get_X_Y()
(in
cosmolopy.density
)
get_omega_k_0()
(in
cosmolopy.distance
)
Gyr_s
(in
cosmolopy.constants
)
H
H100_s
(in
cosmolopy.constants
)
havetffit
(in
cosmolopy.perturbation
)
hubble_z()
(in
cosmolopy.distance
)
havepower
(in
cosmolopy.perturbation
)
hubble_distance_z()
(in
cosmolopy.distance
)
I
integrate()
(in
PiecewisePowerlaw
)
integrate_piecewise()
(in
cosmolopy.utils
)
iPhotonRateDensity()
(in
cosmolopy.luminosityfunction
)
integrate_ion_recomb()
(in
cosmolopy.reionization
)
ionization()
(in
LFHistory
)
iPhotonRateDensity_t()
(in
LFHistory
)
integrate_ion_recomb_collapse()
(in
cosmolopy.reionization
)
ionization_from_collapse()
(in
cosmolopy.reionization
)
iPhotonRateDensity_z()
(in
LFHistory
)
integrate_optical_depth()
(in
cosmolopy.reionization
)
ionization_from_luminosity()
(in
cosmolopy.reionization
)
iPhotonRateRatio()
(in
BrokenPowerlawSED
)
L
L_nu_from_magAB()
(in
cosmolopy.magnitudes
)
light_travel_distance()
(in
cosmolopy.distance
)
lookback_time()
(in
cosmolopy.distance
)
L_nu_from_sfr()
(in
cosmolopy.luminosityfunction
)
linear_coefficients()
(in
Extrapolate1d
)
luminosity_distance()
(in
cosmolopy.distance
)
lambda_Lya_0
(in
cosmolopy.constants
)
load()
(in
Saveable
)
luminosity_wavelength()
(in
BrokenPowerlawSED
)
lambda_NV_0
(in
cosmolopy.constants
)
loadSaveable()
(in
cosmolopy.saveable
)
luminosityfunction
(in
cosmolopy
)
lambdanu()
(in
BrokenPowerlawSED
)
logquad()
(in
cosmolopy.utils
)
LFHistory
(in
cosmolopy.luminosityfunction
)
lookback_integrand()
(in
cosmolopy.distance
)
M
m_H_g
(in
cosmolopy.constants
)
magnitude_AB()
(in
cosmolopy.magnitudes
)
mass_from_sfr()
(in
cosmolopy.luminosityfunction
)
m_He_g
(in
cosmolopy.constants
)
magnitude_AB1450()
(in
cosmolopy.magnitudes
)
mass_to_radius()
(in
cosmolopy.perturbation
)
m_p_g
(in
cosmolopy.constants
)
magnitude_AB_from_L_nu()
(in
cosmolopy.magnitudes
)
Mpc_cm
(in
cosmolopy.constants
)
M_sun_g
(in
cosmolopy.constants
)
magnitudeAB_from_sfr()
(in
cosmolopy.luminosityfunction
)
Mpc_km
(in
cosmolopy.constants
)
MAB0
(in
cosmolopy.magnitudes
)
magnitudes
(in
cosmolopy
)
Myr_s
(in
cosmolopy.constants
)
N
nDotRecMHR()
(in
cosmolopy.reionization
)
Normalize
(in
cosmolopy.utils
)
NullWriter
(in
cosmolopy.saveable
)
norm_power()
(in
cosmolopy.perturbation
)
nu_lambda()
(in
cosmolopy.magnitudes
)
O
O2010_z7
(in
cosmolopy.luminosityfunction
)
omega_M_z()
(in
cosmolopy.density
)
optical_depth_instant()
(in
cosmolopy.reionization
)
P
parameters
(in
cosmolopy
)
perturbation
(in
cosmolopy
)
plotLFevo()
(in
cosmolopy.luminosityfunction
)
params_t()
(in
LFHistory
)
photonRate_wavelength()
(in
BrokenPowerlawSED
)
power_spectrum()
(in
cosmolopy.perturbation
)
params_z()
(in
LFHistory
)
PiecewisePowerlaw
(in
cosmolopy.utils
)
powererror
(in
cosmolopy.perturbation
)
pc_cm
(in
cosmolopy.constants
)
planck_erg_s
(in
BrokenPowerlawSED
)
proper_motion_distance()
(in
cosmolopy.distance
)
Q
quick_age_function()
(in
cosmolopy.distance
)
quick_ion_col_function()
(in
cosmolopy.reionization
)
quick_distance_function()
(in
cosmolopy.distance
)
quick_redshift_age_function()
(in
cosmolopy.distance
)
R
radius_to_mass()
(in
cosmolopy.perturbation
)
redshift_d_light()
(in
cosmolopy.distance
)
recomb_rate_coeff_HG()
(in
cosmolopy.reionization
)
reionization
(in
cosmolopy
)
S
save()
(in
Saveable
)
schechterM()
(in
cosmolopy.luminosityfunction
)
sig_del()
(in
cosmolopy.perturbation
)
saveable
(in
cosmolopy
)
schechterTotLL()
(in
cosmolopy.luminosityfunction
)
sigma_j()
(in
cosmolopy.perturbation
)
Saveable
(in
cosmolopy.saveable
)
schechterTotLM()
(in
cosmolopy.luminosityfunction
)
sigma_r()
(in
cosmolopy.perturbation
)
schechterCumuLL()
(in
cosmolopy.luminosityfunction
)
set_omega_k_0()
(in
cosmolopy.distance
)
sigma_T_cm
(in
cosmolopy.constants
)
schechterCumuLM()
(in
cosmolopy.luminosityfunction
)
sfr_from_L_nu()
(in
cosmolopy.luminosityfunction
)
sigma_T_Mpc
(in
cosmolopy.constants
)
schechterL()
(in
cosmolopy.luminosityfunction
)
sfr_from_mass()
(in
cosmolopy.luminosityfunction
)
T
T2010ICLF
(in
cosmolopy.luminosityfunction
)
tffiterror
(in
cosmolopy.perturbation
)
test_plot_schechter()
(in
cosmolopy.luminosityfunction
)
transfer_function_EH()
(in
cosmolopy.perturbation
)
U
utils
(in
cosmolopy
)
V
vecquad()
(in
cosmolopy.utils
)
virial_mass_HB()
(in
cosmolopy.perturbation
)
virial_temp_HB()
(in
cosmolopy.perturbation
)
virial_mass()
(in
cosmolopy.perturbation
)
virial_temp()
(in
cosmolopy.perturbation
)
volume_radius_dmdr()
(in
cosmolopy.perturbation
)
W
w_gauss()
(in
cosmolopy.perturbation
)
WMAP5_BAO_SN_mean()
(in
cosmolopy.parameters
)
WMAP7_BAO_H0_mean()
(in
cosmolopy.parameters
)
w_tophat()
(in
cosmolopy.perturbation
)
WMAP5_mean()
(in
cosmolopy.parameters
)
WMAP7_ML()
(in
cosmolopy.parameters
)
WiggleZ_fiducial()
(in
cosmolopy.parameters
)
WMAP5_ML()
(in
cosmolopy.parameters
)
write()
(in
NullWriter
)
Y
yr_s
(in
cosmolopy.constants
)
Z
zlinear
(in
cosmolopy.luminosityfunction
)
_
__call__()
(in
BrokenPowerlawSED
)
__init__()
(in
PiecewisePowerlaw
)
__package__
(in
cosmolopy.saveable
)
__call__()
(in
Extrapolate1d
)
__package__
(in
cosmolopy.EH
)
__package__
(in
cosmolopy.utils
)
__call__()
(in
Normalize
)
__package__
(in
cosmolopy
)
__setstate__()
(in
Saveable
)
__call__()
(in
PiecewisePowerlaw
)
__package__
(in
cosmolopy.constants
)
__setstate__()
(in
AgeSpacedRedshift
)
__getstate__()
(in
Saveable
)
__package__
(in
cosmolopy.density
)
_logquad
(in
cosmolopy.utils
)
__init__()
(in
BrokenPowerlawSED
)
__package__
(in
cosmolopy.distance
)
_sigmasq_j_vec
(in
cosmolopy.perturbation
)
__init__()
(in
LFHistory
)
__package__
(in
cosmolopy.luminosityfunction
)
_sigmasq_r_vec
(in
cosmolopy.perturbation
)
__init__()
(in
Saveable
)
__package__
(in
cosmolopy.magnitudes
)
_vec_transfer_func
(in
cosmolopy.perturbation
)
__init__()
(in
AgeSpacedRedshift
)
__package__
(in
cosmolopy.parameters
)
_vecquad
(in
cosmolopy.utils
)
__init__()
(in
Extrapolate1d
)
__package__
(in
cosmolopy.perturbation
)
__init__()
(in
Normalize
)
__package__
(in
cosmolopy.reionization
)
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Author: Kyle King
Date: May 8, 2015
My Second Python Script!
# All the essentials
import numpy as np # np.__version__
import matplotlib.pyplot as plt
import csv
from decimal import *
from pylab import *
plt.close("all")
Question 1
Assess how the dissociation constant (Kd) affects ligand binding to a protein. Specifically, plot the fraction of a protein that is in the bound state (CPL/PTotal) as a function of unbound ligand concentration (CL) for three cases (a) Kd =10 mM; (b) Kd =1 mM; and (c) Kd = 0.1 mM.
# Declare varibales
R = 8.314
Kd = [10, 1, 0.1] # mM
Cl = np.linspace(0.001, 10, num=1000) # ligand concentration from ~0 to 10mM
for n in Kd:
ratio = 1/(1+(1/(n*Cl))) # equation from lecture 19
# Plot function
plot(Cl, ratio)
title('HW20: Q1 The ratio of CPL/PTotal')
xlabel('Cl')
ylabel('Ratio of CPL/PTotal')
legend(Kd)
grid(True)
# show()
Question 2
Studies with the enzyme tyrosyl-tRNA synthetase indicate that the enzyme can selectively bind the tyrosine moiety relative to the phenylalanine moiety by a factor of 10^5 at 300 K. What is the difference in binding free energy and what types of interactions could be responsible for such a difference?
KaFactor = pow(10, 5)
deldelG = -R*300*log(KaFactor)/1000 # kJ/mole
print("The difference in binding free energy is %d kJ/mole" % deldelG)
print("This could be the result of a difference in one hydrogen bond (about 5 - 30 kJ/mole)")
The difference in binding free energy is -28 kJ/mole
This could be the result of a difference in one hydrogen bond (about 5 - 30 kJ/mole)
Question 3
Several avidin-biotin binding systems have been studied (e.g., variant proteins and ligands) at 300 K. The binding constant (Ka) and binding enthalpy have been measured along with the force required to mechanically unbind the protein-ligand complex (Fu). From the data below, does the unbinding force correlate better with the free energy of binding or the enthalpy of binding? (Moy et al. Sci. 266:257 (1994)).
def getNumericColumn(filename, column):
results = csv.reader(open(filename), delimiter=",", quoting=csv.QUOTE_NONNUMERIC)
return [result[column] for result in results]
# Import variables from csv file
filename = 'Q2data.csv'
# Convert to int for indexing
Count = np.array(map(int, getNumericColumn(filename, 0))) # M^-1
KaBase = getNumericColumn(filename, 1) # M^-1
KaPow = getNumericColumn(filename, 2)
Fu = getNumericColumn(filename, 3) # pN
DelH = getNumericColumn(filename, 4) # Kcal/mol
# Create Empty Array Ka
Ka = [0]*(len(Count))
# Fill array with values from csv file
for i in Count:
Ka[i] = KaBase[i]*pow(10, KaPow[i])
DelG = -R*300*log(Ka)/1000 # kJ/mole
fig2 = plt.figure()
plt.scatter(DelG, Fu)
title('Free Energy versus Unbinding Force')
xlabel('Free Energy of Binding (kJ/mol)')
ylabel('Unbinding Force (Fu) in pN')
fig3 = plt.figure()
plt.scatter(DelH, Fu)
title('Binding Enthalpy versus Unbinding Force')
xlabel('Binding Enthalpy (kcal/mol)')
ylabel('Unbinding Force (Fu) in pN')
# plt.show()
print('The Binding Enthalpy has a much stronger coorelation with Fu')
The Binding Enthalpy has a much stronger coorelation with Fu
Question 4
See attached handwritten notes