Synopsis 1-12 Flashcards
what is biophysics
interdisciplinary science between bio and physics
uses scientific problems and approaches, not applied methods
its fundamentals are applied in other discipline
what are the subareas in biophysics
environmental = interactions of various physical influences on physiological functions
molecular=studies physiochemical structures of biological molecules
cellular=studies cellular structures and bioenergetics
microphysical?
individual behaviour of single small particles, they are stochastic, randomly distributed
stochastic?
random behavior
macrophysical behavior
the behaviour of large bodies rules by laws of classical physics, deterministic behaviour, EG pressure, temp, vol
anisotropy meaning
property of a material which allows it to assume different properties in different directions, opposed to isotropy
isotropy
uniform in all directions,
intramolecular bonds
covalent = 2 non-metal atoms, share unpaired electrons, the greater the probability of the presence of electron pair, the stronger the electronegativity
ionic bonds=transfer of electrons from 1 atom to another to cause a full separation of charges so that the ions are electronegatively attracted to each other
TD system
region of the universe under study, separated from surroundings by a boundary
types of TD system
isolated = no exchange of matter/energy between system and surroundings
closed=exchange of energy, not matter between system and surroundings
open=matter and energy able to cross boundary btw system and surroundings
homogenous
the system has the same chemical composition throughout
TD state
instantaneous quantitative description of a system with a set number of variables held constant
intensive variables
physical quantities, the value doesn’t depend on AOS, depends on nature EG Temp, Press, Density, Viscosity, Conc, moles
extensive variables
physical quantity, value is proportional to size of system it describes EG mass, vol, entropy
TD Equil
no net macroscopic flows of matter or of energy, either within a system or between systems
conjugate variables
TD systems transfer energy due to generalized force to cause generalized displacement, in which the product of the 2 is the amount of energy transferred EG Pressure+Vol, Temp+Entropy, Chemical Potential+particle no.
TD Process
energetic evolution of TD system, proceeding from initial to final state, it is reversible
EG of TD process
Isobaric=contant P isochoric=contant V isothermal=constant T isoentropic=constant S isoenthalpic=constant H adiabetic=w/o loss or gain of Heat energy Q
Equilibrium TD
Systematic study of transformations of matter and energy in systems as they approach equilibrium
the mathematical formulation of the 1st law of TD
dQ=dU+dW
dQ=Change in heat energy in and out of the system
dW=Change in work done by or on the system
dU=Change in system’s internal energy
1st law of TD
Total energy of isolated system always remains constant, the energy may change from one form to another, but cannot be created nor destroyed.
If a quantity of energy disappears, the exact equivalent quantity of some other form of energy must be produced
limitations of 1st law of TD
No conditions of mutual convertability=so it doesn’t specify under what circumstances or extent it is possible to convert one form of energy to another.
The law says the amount of heat energy lost = it is gained, doesn’t say heat must flow spontaneously from hot to cold
Different forms of energy can be conserved readily into heat but it is impossible to convert heat completely into mechanical energy/work
2nd law of TD
Total Entropy of an isolated system will never decrease over time. In a reversible process, it is constant.
mathematical formula of 2nd law of TD in a reversible process
dS=dQ/T
mathematical formula of 2nd law of TD in a irreversible process
dS>dQ/T
phenomenological definitions of entropy
impossible:
- for self-acting machine unaided by external forces to convey heat from low to high temp
- to lift weight and cool body w/o leaving any change
- to convert heat into equivalent amount of work w/o producing other change to a system
spontaneous reaction=total S will increase
Boltzmann distribution of entropy
Shows relationship between entropy and number of ways molecules of TD system can be arranged
entropy
measure of degree of randomness/disorder of a system
TD probability
S=klnW, entropy as function of W, relates no. of microstates of a system to macrostate
boltzmann constant
k [J/K] proportionality factor
microstate
specific microscopic configuration of TD System that system occupies w/ certain probabilities
macrostate
characterized by probability distribution of possible states across certain statistical ensemble of all microstates
Information
I=f(P), function of mathematical probability
who is shannon
introduces parameter into info theory related to entropy called information
probability
no. of favourable cases over greatest possible no. of cases
shannon equation of info theory
I=KlnP [bits or J/K]
Used to calculate info content of protein or nucleic acid by using statistical record of frequency in occurence of individual AA in proteins, which provides P for prescence of given AA at certain locus. By using Shannon’s Equation we can find info content of each monomer calculated
maxwell’s demon
creature able to slide between 2 rooms filled w/ gas where the pressure and temp is in equilibrium.
it observes direction and velocity accurately of molecules in the rooms and opens the door to allow faster molecules in 1 room and slower molecules in another.
this heats up 1 chamber, this decreases entropy of total system, which violates the 2nd law of TD
TD potential
quantitative measure of stored energy in system, used to measure energy in systems as they evolve from initial to final state
internal energy U
energy contained w/i TD system, the energy necessary to create or prepare the system in any given internal state
enthalpy H
The sum of internal energy and the work required to achieve its pressure and volume of a TD system
helmholtz free energy F
measures useful work from closed TD System
gibbs free energy G
amount of energy capable of doing work during chemical reaction
when dG = -ive
exergonic reaction, spontaneous, loss of free energy
when dG= +ive
endergonic reaction, non-spontaneous, reaction will not process as written
electric potential
Ep/q [V]
used to explain origin of electric field
Non-Equil TD
System not in TD Equil, but broken into subsystems small enough to be in equil but large enough for TD laws to be applicable in them
TD forces
differences of intensive parameters to cause flow of extensive variables
Phenomenological law
J=LX
J=Flux EG. Heat, Mass, Electricity
L= Proportionality constant/Transport Coefficient
X=Driving force EG. Temp Grad, Conc Grad, Potential Grad
Onsager’s coefficient
shows that near equilibrium, flux matrix is symmetric, it exists only for conjugated fluxes
conjugated flux
pair of variables EG T&S, P&V
sigma meaning in entropy
entropy production per unit time
dSi means
entropy production arising due to transfer of heat from phase 1 and phase 2 due to temperature difference
stationary state
system’s macroscopic properties don’t change w/ time, microscopic/intensive variables does change w/ time
global equil
free energy doesn’t alter, 1 minimum, can bring other systems into equilibrium
local equil
2 or more minima, seperated by large energy barriers
3rd law of TD is about
absolute 0 temp, the S of a system approaches constant value as Temp apporaches absolute 0
0th law of TD
if 2 bodies are the TD Equil with a 3rd body, they are also in Thermal Equil with each other
