MDC Biophysics notes

Biophysics MDC Notes

What is Biophysics?

Biophysics is the science that explains biological structure and function using the concepts and techniques of physics and physical chemistry.

Unit - I: Building blocks and Living state interactions

Biophysical Definition of Life:

Life is a highly ordered, self-organizing, self-regulating system composed of molecules that can harvest energy, maintain homeostasis, grow, adapt, respond to stimuli, and reproduce, governed by the principles of physics and chemistry.

Biophysics sees life not as a mystical entity, but as a system of matter and energy interacting through physical laws, capable of self-sustenance, replication, and evolution.

As per biology and biophysics, following are the essential atoms, ions and molecules for life:

1. Essential Atoms (Elements) for Life

These atoms form the building blocks of biological molecules:

Element	Symbol	Role
Carbon	C	Backbone of all organic molecules (proteins, carbs, lipids, nucleic acids)
Hydrogen	H	Found in water and all organic compounds
Oxygen	O	In water, respiration, and organic compounds
Nitrogen	N	In amino acids, proteins, DNA, RNA
Phosphorus	P	In DNA, RNA, ATP, phospholipids
Sulfur	S	In some amino acids (cysteine, methionine) and proteins
Calcium	Ca	Signaling, bone structure, enzyme cofactor
Potassium	K	Nerve function, osmotic balance
Sodium	Na	Nerve impulse transmission, osmotic balance
Magnesium	Mg	Enzyme cofactor, stabilizes ATP and nucleic acids
Iron	Fe	Oxygen transport (hemoglobin), electron transport chain
Zinc	Zn	Enzyme function, gene expression regulation

2. Essential Ions in Life (Electrolytes and Trace Ions)

Ion	Symbol	Biological Function
Sodium ion	Na⁺	Maintains membrane potential, nerve impulses
Potassium ion	K⁺	Intracellular fluid balance, nerve/muscle function
Calcium ion	Ca²⁺	Muscle contraction, blood clotting, signaling
Magnesium ion	Mg²⁺	Enzyme activation, DNA/RNA stabilization
Chloride ion	Cl⁻	Maintains osmotic pressure, stomach acid (HCl)
Phosphate ion	PO₄³⁻	Energy transfer (ATP), nucleic acids
Hydrogen ion (proton)	H⁺	pH balance, drives ATP synthesis (chemiosmosis)
Iron ion	Fe²⁺/Fe³⁺	Electron transport, oxygen binding in hemoglobin
Zinc, Copper, Manganese, Cobalt	Zn²⁺, Cu²⁺, Mn²⁺, Co²⁺	Enzyme cofactors, redox reactions

3. Essential Molecules for Life

These are biomolecules composed of the atoms above:

a) Water (H₂O) – Medium for biochemical reactions, thermoregulation

b) Carbohydrates – Energy (glucose), structure (cellulose, chitin)

c) Proteins – Enzymes, transport, signaling, structure

d) Lipids – Membranes, energy storage, hormones

e) Nucleic Acids (DNA, RNA) – Genetic information and protein synthesis

f) ATP (Adenosine Triphosphate) – Universal energy currency

g) Vitamins & Coenzymes – Assist enzymatic reactions

h) Hormones – Chemical messengers (e.g., insulin, adrenaline)

Forces and Molecular Bonds as Living State Interactions

In biophysics, life is understood as a dynamic state maintained by physical and chemical interactions, especially molecular forces and bonds. These interactions determine the structure, stability, and function of biological molecules and, ultimately, the processes of life.

1. Types of Molecular Bonds and Forces in Living Systems

A. Covalent Bonds

·  Strongest type of chemical bond.

·  Atoms share electrons (e.g., C–C, C–H, C–O).

·  Examples:

o Backbone of DNA and proteins.

o Peptide bonds between amino acids.

o Phosphodiester bonds in DNA/RNA.

B. Ionic Bonds (Electrostatic Interactions)

·    Attraction between oppositely charged ions (e.g., Na⁺ and Cl⁻).

·    Weaker in aqueous environments (like inside cells).

·    Important in:

o   Enzyme-substrate binding.

o   Stabilizing protein structures (e.g., salt bridges).

C. Hydrogen Bonds

·    Occur between a hydrogen atom and an electronegative atom (like O or N).

·    Weaker than covalent but essential for:

o        Base pairing in DNA (A=T, G≡C).

o        Protein folding and secondary structure (e.g., α-helix, β-sheet).

o        Properties of water (solvent of life).

D. Van der Waals Forces

• Weak, transient interactions due to temporary dipoles.
• Important in:

o Molecular recognition (e.g., enzyme-substrate fit).

o Protein stability.

o Lipid interactions in membranes.

E. Hydrophobic Interactions

• Nonpolar molecules avoid water and cluster together.
• Crucial in:

o   Protein folding (nonpolar side chains cluster inward).

o   Formation of lipid bilayers in cell membranes.

Electric Dipole as a Living State Interaction:

In biophysics, an electric dipole is a pair of equal and opposite electric charges separated by a small distance. Electric dipoles are fundamental to many biological molecules and processes, especially in polar molecules, membrane potentials, and molecular interactions.

1. What is an Electric Dipole?

An electric dipole consists of two charges +q and –q separated by a distance d, giving rise to a dipole moment (μ).

Dipole Moment (μ):

μ=q×d

·       It’s a Vector quantity (points from – to +)

• Measured in Debye (D) in molecular biology

2. Electric Dipoles in Biological Molecules

A. Water (H₂O) – The Universal Dipole

• Oxygen is more electronegative → pulls electrons → partial charges (δ⁺ on H, δ⁻ on O).
• Water is a permanent dipole → responsible for:

o     Hydrogen bonding

o     Solvent properties

o     Protein folding and enzyme activity

B. Peptide Bonds and Proteins

• The C=O and N–H groups in peptides are dipolar.
• These dipoles align to form:
• α-helices
• β-sheets
• Helps stabilize protein structure through dipole-dipole interactions and hydrogen bonds.

C. Phospholipids in Cell Membranes

• Phosphate head = polar/dipolar
• Fatty acid tails = nonpolar
• The dipolar nature of the head groups drives bilayer formation, essential for:
• Membrane structure
• Transport
• Signal transduction

D. DNA and RNA

• Phosphate backbone and base pairs create electric dipoles.
• Dipole interactions influence:
• Stability
• Replication
• Protein-DNA binding

3. Dipole Interactions in Living Systems

Types of Dipole Interactions:

Interaction Type	Description	Biological Example
Dipole–Dipole	Between two polar molecules	Protein-protein interactions
Dipole–Induced Dipole	Polar molecule induces dipole in nonpolar one	Enzyme-substrate fit
Ion–Dipole	Ion interacts with dipolar molecule	Na⁺ with water in cytoplasm

4. Role in Cellular Functions

A. Membrane Potentials

• Lipid bilayers with dipolar heads align and affect ion transport.
• Helps maintain resting membrane potential and nerve impulse transmission.

B. Molecular Recognition

• Dipole interactions help molecules recognize and bind to specific partners:
• Hormone-receptor interaction
• Antibody-antigen binding

C. Enzyme Catalysis

• Active sites often use polar residues and dipolar interactions to position substrates.

5. Living State as a Dynamic Dipole Network

• The living state is a non-equilibrium system.
• Maintained by organized interactions among thousands of dipolar molecules in:
• Cytoplasm (polar environment)
• Membranes
• Nucleic acids
• Protein complexes

Casimir Interaction in Biophysics and Living Systems

The Casimir interaction (or Casimir effect) is a quantum physical phenomenon that arises due to vacuum fluctuations of the electromagnetic field between two closely spaced, uncharged conducting plates.

Though it originated in quantum electrodynamics (QED), its relevance to biology and biophysics is emerging in nanoscale systems, such as proteins, membranes, and DNA.

1. What is the Casimir Effect?

The Casimir effect is an attractive (or sometimes repulsive) force between two neutral, closely spaced surfaces in a vacuum, caused by quantum fluctuations of the electromagnetic field. 

Casimir Force Formula:

For two parallel, uncharged, perfectly conducting plates in a vacuum:

F=−π²ℏc/240 d⁴

Where:

• F = force per unit area
• ℏ = reduced Planck constant
• c = speed of light
• d= distance between the plates

2. Origin of Casimir Force

• Even in a vacuum, quantum mechanics predicts that virtual particles and fluctuating fields exist.
• When two plates are placed close together, some fluctuations are excluded, altering energy density between and outside the plates.
• This results in a net attractive force.

3. Casimir Interactions in Biological Systems

Note:

Casimir forces are very weak and short-ranged (significant only at nanometer separations), but in biological nanoscale environments, they may contribute to:

A. Protein Folding and Interactions

• Proteins fold into compact structures with nanometer-level proximity of amino acid chains.
• Casimir-like forces may contribute subtly to stabilization or misfolding phenomena.

B. DNA Packing

• In the nucleus or virus capsids, DNA strands are packed extremely tightly.
• Casimir forces may influence the packing energy landscape.

C. Membrane Interactions

• Cell membranes, lipid bilayers, or organelle surfaces at nanometer distances may experience Casimir–van der Waals type forces.
• Important in membrane fusion, vesicle formation, or cell adhesion.

D. Nanomedicine and Nanodevices

• In drug delivery nanoparticles or biosensors, Casimir forces can affect:
• Adhesion
• Surface interactions
• Function of nanostructured biomaterials

Unit – II: Living State Thermodynamics:

Heat Transfer in Biomaterials and Mechanisms

Heat transfer in biomaterials refers to how thermal energy moves through or within biological tissues and synthetic materials used in medical and biotechnological applications. This is crucial in biomedical engineering, cryopreservation, hyperthermia therapy, tissue engineering, and implants.

Major Mechanisms of Heat Transfer in Biomaterials

There are three fundamental modes of heat transfer that apply to biomaterials:

1. Conduction

• Definition: Transfer of heat through a material without movement of the material itself.
• Mechanism in biomaterials:
• Dominant in solid tissues (bone, skin, muscles) and biomaterial implants.
• Heat moves via vibrations of molecules and free electrons (in metals).
• Key factors:
• Thermal conductivity (k) of material (e.g., bone: ~0.4–0.6 W/m·K; fat: ~0.2 W/m·K).
• Water content – tissues with more water (e.g., muscle) conduct better than fatty tissues.
• Equation:

Q = −k (dT/dx)

where q is the heat flux, k is thermal conductivity, and dT/dx​ is the temperature gradient.

2. Convection

• Definition: Heat transfer via fluid motion (blood, lymph, interstitial fluid).
• Mechanism in biomaterials:
• Especially important in perfusion of tissues, where blood flow distributes heat.
• Affects cooling/heating rates during surgeries or thermal therapies.
• Types:
• Natural convection: Due to density differences (e.g., in heated blood).
• Forced convection: Due to blood flow or external pumping.
• Biological Example: Blood flow regulating tissue temperature during fever or exercise.

3. Radiation

• Definition: Emission or absorption of electromagnetic waves (infrared).
• Mechanism in biomaterials:
• Less significant inside tissues but important at tissue-air interfaces (e.g., skin).
• Plays a role in infrared thermography and laser therapies.
• Example: Skin radiates heat to surroundings or absorbs infrared laser in treatments.

Special Heat Transfer Mechanisms in Biomaterials

➤ Phase Change (Latent Heat)

• In cryopreservation, heat is absorbed or released during freezing/thawing.
• Water-to-ice transition involves latent heat, impacting cell viability.

➤ Metabolic Heat Generation

• Living tissues produce heat due to cellular respiration.
• Important in thermal modeling of tissues:

➤ Bioheat Equation (Pennes’ Model)

Used to model heat transfer in living tissues:

ρc (∂T/∂t)​ =∇⋅(k∇T) + ω_b c_b (T_a − T) + Q _met + Q _ext

Where:

• ρ – tissue density and
• c - specific heat
• T – temperature
• ω_b & c_b​ – blood perfusion rate and blood specific heat
• Ta – arterial blood temperature
• Q_met​ – metabolic heat
• Q_ext​ – external heat sources (e.g., lasers, ultrasound)

Applications of Heat Transfer in Biomaterials

Application	Role of Heat Transfer
Hyperthermia cancer therapy	Targeted heating of tumors using RF/microwave
Cryopreservation	Controlled freezing to avoid ice damage
Prosthetics and implants	Materials chosen to avoid excessive heating or chilling
Laser surgeries	Requires precise thermal modeling to avoid collateral damage
Tissue engineering	Bioreactor temperature regulation for cell growth

Thermodynamic Equilibrium in Biophysics

Thermodynamic equilibrium is a fundamental concept in biophysics, describing the state in which all macroscopic flows of energy and matter have stopped, and the system's properties are stable over time.

What is Thermodynamic Equilibrium?

A system is in thermodynamic equilibrium when:

1.    Thermal equilibrium – No temperature gradients exist.

2.    Mechanical equilibrium – No pressure gradients or unbalanced forces.

3.    Chemical equilibrium – No net chemical reactions or diffusion.

4.    Phase equilibrium – Coexisting phases (e.g., solid-liquid) are stable.

In short: The system has no net flow of heat, mass, or energy.

Importance in Biophysics

In biophysics, thermodynamic equilibrium helps understand how biological systems store, transform, and transfer energy.

Examples in Biological Context

Biological Process	Relevance of Equilibrium
Cell Membrane Potential	Cells maintain ion gradients → not at equilibrium (but in steady state)
Protein Folding	Folded state often represents a local energy minimum (quasi-equilibrium)
Ligand Binding	Reaches chemical equilibrium between free and bound states
Enzyme Reactions	Rate of forward = rate of reverse at equilibrium
Diffusion of molecules	Final state is concentration equilibrium
Osmosis	Solvent moves until osmotic pressure equilibrium is reached

Difference: Equilibrium vs Steady State

• Equilibrium:
• No net energy/matter flow
• System is static
• Maximum entropy
• e.g.: dead cell (no gradients, no work)
• Steady State:
• Constant energy/matter input and output
• System maintains gradients
• Low entropy
• e.g.: living cell (ATP production, ion transport)

Living systems are rarely at equilibrium, but instead in dynamic steady states to stay alive.

Entropy and the Second Law of Thermodynamics:

1. What is Entropy?

Entropy (S) is a measure of:

• Disorder or randomness in a system
• Number of microscopic configurations that correspond to a macroscopic state
• Energy dispersion — how spread out the energy is in a system

Thermodynamic Definition:

ΔS = q_rev/T

Where:

• ΔS = change in entropy
• q_rev = reversible heat exchange
• T = absolute temperature in kelvin (K)

In Biophysics:

• Protein folding reduces entropy of the protein but increases water entropy → net increase in total entropy
• Diffusion increases entropy as molecules move from order to disorder.
• Living systems constantly fight entropy by using energy (e.g., from ATP) to maintain order.

2. Second Law of Thermodynamics

Statement:

"In any natural thermodynamic process, the total entropy of an isolated system always increases or remains constant."

In simpler terms:

• Energy spontaneously spreads out, unless prevented from doing so.
• Systems tend to move toward maximum entropy.

Reversible vs Irreversible Processes:

Process Type	Entropy Change
Reversible	ΔStotal=0\Delta S_{\text{total}} = 0ΔStotal​=0
Irreversible (natural)	ΔStotal>0\Delta S_{\text{total}} > 0ΔStotal​>0

Entropy in Biological Systems

Example	Entropy Concept
Cell death	Disorder increases → entropy increases
ATP hydrolysis	Energy release → increases entropy of surroundings
Metabolism	Converts ordered molecules (glucose) into CO₂ + H₂O + heat (higher entropy)
Protein folding	Local order ↑, but water entropy ↑ more → total entropy still ↑
Osmosis	Solute moves to even out concentration → entropy ↑

Statistical View (Boltzmann Entropy)

S= k_B lnΩ

Where:

• S = entropy
• k_B = Boltzmann constant
• Ω = number of microstates

More microstates → more entropy.

Do Living Things Violate the Second Law?

No.
Living organisms:

• Maintain internal order (low entropy)
• But they export entropy to their surroundings (e.g., heat, waste)
• Net entropy of the universe still increases

Life exists in a non-equilibrium steady state — using energy to resist entropy.

Thermodynamic Criteria for Equilibrium

A system is in equilibrium if:

• ΔG=0 → No net change in Gibbs free energy
  (for constant T and P)
• dU=0 for isolated system → Internal energy is constant
• Entropy S is maximized for isolated system

Unit - III: Chemical Thermodynamics in Open System

What is an Open System?

·         A system = the part of the universe we are studying.

·         An open system can:

o    Exchange energy (heat Q or work W)

o    Exchange matter (mass or particles)
with its surroundings.

Examples:

·         A boiling pot of water without a lid (steam and heat escape)

·         A human body (takes in oxygen, food; releases heat, CO₂, sweat)

Extensive properties:

An extensive property is a physical property of a system that depends on the amount (size, mass, or number of moles) of matter present. Examples of extensive property are internal energy, enthalpy, entropy, free energy etc.

Partial molar properties:

Partial molar properties are thermodynamic quantities that describe how an extensive property of a solution changes when you add a very small (infinitesimal) amount of one component, while keeping temperature, pressure, and the amounts of all other components constant.

Definition

If M is an extensive property of a mixture (such as volume V, Gibbs free energy G, enthalpy H, or entropy S), then the partial molar property of component i, denoted as Mi, is defined as:

Where:

• n_i​ = number of moles of component i
• T = temperature (constant)
• P = pressure (constant)
• n_j≠i​ = moles of all other components (kept constant)

It represents the contribution per mole of component iii to the total property of the mixture.

Key Idea

• Extensive properties (like V,G,H,S) depend on both the total number of moles and the composition.
• The partial molar property tells you how much that property changes if you add one mole of a specific component to the mixture.

Examples

1.    Partial molar volume:
Change in total volume when 1 mole of i is added at constant T,P and composition of others fixed.

2.    Partial molar Gibbs free energy :
Also called the chemical potential:

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