Biolist stat mech

Question 1

detailed balance

Answer 1

the probability flux forward and backward are equal

Question 2

in MD what is the constants for the microcanonical ensembles?

Answer 2

NVE

adiabatic process

Question 3

canonical ensemble in MD

Answer 3

NVT

uses a specific thermostat
i.e. Nose-Hoover or Langevin

Question 4

What is the NPT ensemble in MD

Answer 4

Isobaric and isothermal

closest to lab conditions with an open flask

Question 5

length of long range interactions

Answer 5

r^(-d)

Question 6

HP model

Answer 6

only considers hydrophobic (H) or polar

one energy units is given for each HH contact
It’s done on a ladder type model

Question 7

REM

Answer 7

a stochastic process
energies are random variable E = Normal(0,N/2)

-most basic is zero mean and N/2 variance

it can be used with partition function

Question 8

spin glasses

Answer 8

energy (conformation) and many possible conformatinos at a single energy

E = -sum(e(a))- sum(J(a)) -sum(K(a))

e(a) is primary structure
J(a) is secnondary structure
K(a) is tertiary structure

random energy model with uncorrelated spins

Question 9

GNK model

Answer 9

K corresponds to ruggedness of landscape and number of mutations
K = 0,N-1

N is length of path?

This describes the genotypes linked by mutational paths

For studying ability of a protein to mutate

Question 10

basic features of immune system

Answer 10

can discriminate, has specificity, and has memory