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PROTEIN PHYSICS LECTURE 8. THERMODYNAMISC & STATISTICAL PHYSICS. WHAT IS “TEMPERATURE”? EXPERIMENTAL DEFINITION :. EXPERIMENTAL DEFINITION. = t, o C + 273.16 o. WHAT IS “TEMPERATURE”?. THEORY Closed system: energy E = const. S ~ ln[M].

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PROTEIN PHYSICS LECTURE 8

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Protein physics lecture 8

PROTEIN PHYSICS

LECTURE 8


Protein physics lecture 8

THERMODYNAMISC

&

STATISTICAL PHYSICS


Protein physics lecture 8

WHAT IS “TEMPERATURE”?

EXPERIMENTAL DEFINITION :

EXPERIMENTAL DEFINITION

= t,oC + 273.16o


Protein physics lecture 8

WHAT IS “TEMPERATURE”?

THEORY

Closed

system:

energy

E = const

S ~ln[M]

CONSIDER: 1 state of “small part” with  & all

states of thermostat with E-. M(E-) = 1•Mth(E-)

St(E-) = k •ln[Mt(E-)]  St(E) - •(dSt/dE)|E

Mt(E-) = exp[St(E)/k] • exp[-•(dSt/dE)|E/k]


Protein physics lecture 8

All-system’s states with E have equal probabilities

For “small part’s” state: depends on e:

COMPARE:

Probability1(1) = Mt(E-1)/SE’M(E’) ~

exp[St(E)/k] • exp[-1• (dSt/dE)|E/k]

and

Probability1(1) ~ exp(-1/kBT) (BOLTZMANN)

One has: (dSt/dE)|E = 1/T

k = kB

______________________________________________________________

  -kBT, M  Mexp(1)  M2.72


Protein physics lecture 8

(dSth/dE) = 1/T

P1(1) ~ exp(-1/kBT)

Pj(j) = exp(-j/kBT)/Z(T); j Pj(j)  1

Z(T) = i exp(-i/kBT) partition function

СТАТИСТИЧЕСКАЯ СУММА


Protein physics lecture 8

Along tangent: S-S(E1)= (E-E1)/T1

i.e.,F = E - T1S= const (= F1 = E1 - T1S1)

stable

Unstable (explodes, V → ): Unstable (fells):

unstable


Protein physics lecture 8

Separation of potential energy

in classic (non-quantum) mechanics:

P() ~ exp(-/kBT) Classic:=COORD+ KIN

KIN= mv2/2 : does not depend on coordinates

Potential energy COORD: depends only on coordinates

P() ~ exp(-COORD/kBT) • exp(-KIN/kBT)

Z(T) = ZCOORD(T)•ZKIN(T)  F(T) = FCOORD(T)+FKIN(T)

========================================================================================================================

Elementary volume: (mv)x = ħ  (x)3 =(ħ/|mv|)3


Protein physics lecture 8

IN THERMAL EQUILIBRIUM:

TCOORD=TKIN=T

We may consider further

only potential energy:

EECOORD

MMCOORD

S(E)SCOORD(ECOORD )

F(E)FCOORD , etc.


Protein physics lecture 8

TRANSITIONS:

THERMODYNAMICS


Protein physics lecture 8

gradual transition

“all-or-none” (or first order)

phase transition

coexistence

(T/T*)(E/kT*)~1

coexistence

& jump


Protein physics lecture 8

“all-or-none” (or first order) phase transition

F(T1)


Protein physics lecture 8

Second order phase transition

change

Not observed in proteins up to now: they are too small


Protein physics lecture 8

TRANSITIONS:

KINETICS


Protein physics lecture 8

n#=nexp(-F#/kBT)

n#

n

TRANSITION TIME:

t01 = t0#1 =

= # (n/n#)=#exp(+F#/kBT)


Protein physics lecture 8

PARALLEL REACTIONS:

TRANSITION RATE = SUM OF RATES

(or: the highest rate)

RATE = 1/TIME


Protein physics lecture 8

#

#

_

start

finish

CONSECUTIVE REACTIONS:

TRANSITION TIME  SUM OF TIMES

t0… finish = t0#1 finish + t0#2 finish + …


Protein physics lecture 8

#main

#main

_

_

“trap”: on

“trap”: out

start

start

finish

finish

TRANSITION TIME IS ESSENTIALLY

EQUAL FOR “TRAPS” AT AND OUT OF PATHWAYS OF CONSECUTIVE REACTIONS:

TRANSITION TIME  SUM OF TIMES

(or: the longest time)


Protein physics lecture 8

DIFFUSION:

KINETICS


Mean kinetic energy of a particle mv 2 2 k b t j p j j j v 2 v x 2 v y 2 v z 2 maxwell

Mean kinetic energy of a particle:mv2/2 ~ kBT<> = j Pj(j) j v2 = (vX2)+(vY2)+(vZ2)Maxwell:


Protein physics lecture 8

Friction stops a molecule within picoseconds:

m(dv/dt) = -(3D)v [Stokes law]

D – diameter;

m ~ D3 – mass;

 – viscosity

tkinet 10-13 sec  (D/nm)2in water

During tkinet the molecule moves somewhere by Lkinet ~ v•tkinet

Then it restores its kinetic energy mv2/2 ~ kBT from thermal kicks of other molecules, and moves in another random side

CHARACTERISTIC DIFFUSION TIME: nanoseconds


Protein physics lecture 8

Friction stops a molecule within picoseconds:

tkinet 10-13 sec  (D/nm)2in water

During tkinet the molecule moves somewhere by Lkinet ~v•tkinet

Then it restores its kinetic energy

mv2/2 ~ kBT from thermal kicks

of other molecules, and moves in

another random side

CHARACTERISTIC DIFFUSION

TIME: nanoseconds

The random walk allows the molecule

to diffuse at distance D (~ its diameter)

within ~(D/L kinet)2steps, i.e., within

tdifft tkinet•(D/Lkinet)2 4•10-10 sec  (D/nm)3in water


Protein physics lecture 8

For “small part”: Pj(j) = exp(-j/kBT)/Z(T);

Z(T) = j exp(-j/kBT)

j Pj(j) = 1

E(T) = <> = j j Pj(j)

if allj =: #STATES = 1/P, i.e.: S(T) = kBln(1/P)

S(T) = kB<ln(#STATES)>= kBj ln[1/Pj(j)]Pj(j)

F(T) = E(T) - TS(T) = -kBT  ln[Z(T)]

STATISTICAL MECHANICS


Protein physics lecture 8

Thermostat: Tth = dEth/dSth

“Small part”: Pj(j,Tth) ~ exp(-j/kBTth);

E(Tth) = j jPj(j,Tth)

S(Tth) = kBj ln[1/Pj(j,Tth)]Pj(j,Tth)

Tsmall_part = dE(Tth)/dS(Tth) = Tth

STATISTICAL

MECHANICS


Protein physics lecture 8

Along tangent: S-S(E1)= (E-E1)/T1

i.e.,

F = E - T1S= const (= F1 = E1 - T1S1)


Protein physics lecture 8

Separation of potential energy

in classic (non-quantum) mechanics:

P() ~ exp(-/kBT) Classic:=COORD+ KIN

KIN= mv2/2 : does not depend on coordinates

Potential energy COORD: depends only on coordinates

P() ~ exp(-COORD/kBT) • exp(-KIN/kBT)

ZKIN(T) =K exp(-K/kBT): don’t depend on coord.

ZCOORD(T) =Cexp(-C/kBT): depends on coord.

Z(T) = ZCOORD(T)•ZKIN(T)  F(T) = FCOORD(T)+FKIN(T)

========================================================================================================================

Elementary volume: (mv)x = ħ  (x)3 =(ħ/|mv|)3


Protein physics lecture 8

P(KIN+COORD) ~ exp(-COORD/kBT)•exp(-KIN/kBT)

P(COORD) = exp(-COORD/kBT) / ZCOORD(T)

ZCOORD(T) =Cexp(-C/kBT): depends ONLY

on coordinates

P(KIN) = exp(-KIN/kBT) / ZKIN(T)

ZKIN(T) =K exp(-K/kBT): don’t depend on coord.

T<0: unstable (explodes)

<KIN>   at T<0

due to

P(KIN) ~ exp(-KIN/kBT)


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