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What is SOFT MATTER ?                           What is Self-assembly ? 

 

FUN: Youtube videos  on soft-matter properties.

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My recent research on DNA organization explained in a layman's language (2020):

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DNA Organization while replication is in progress : explained for the layman (2022).

 

NPTEL-    Introductory video & Computational Physics Lectures

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Brief lectures on my recent research:

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Soft and Living Matter research groups around the world

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LivinG Matter: subdiscipline of physics since 2022: increased focus in USA/Europe (Prof. Bialek-Princeton).

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Soft Matter and Living Matter research groups of India (incomplete list)

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Research Funding :

      

    DST-India, SERB (2015-2018) : Rs 3.3 million (33 lakhs approximately)

    DBT-India (2017-2020) :  Rs 4.2 million (42 lakhs approximately)

    MATRICS project (2020-2022): Rs. 2 lakhs per year.

    DST-SERB project (with V. Chikkadi: 2022-2024)  on Active Matter: Modeling + Exp: Rs 7 million

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ONGOING  RESEARCH:

1. Heirarchical Self Assembly: How do Nanoparticles self-organize to form different nano-structures in a  matrix of Self-assembled polymers?  (by Shaikh Mubeena).

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2.  How does bacterial DNA gets organized at micron length scales?

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One knows that the DNA  molecule is a double helix at nano-meter length scales, but how do we explain DNA organization at large (micron) length scales. Is there some organization at all, or is it random coil changing configurations due to Brownian motion ?

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Left pic: Some segments are found spatially closer to certain other segments in a minimalist model of the DNA-Polymer.    Bright patches correspond to high probabilities of certain segments to be closer.            

 Right pic: organization of a simple DNA model: our simulations (by Tejal Agarwal).

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3.  How do entropic forces help segregate two conjoined ring-polymers, which are initially  in a mixed state ? 

When the system reaches  equilibrium  (at end of simulation), the two polymers occupy different halves of a cylinder: implications in bacterial DNA segregation after replication. 


See  Movie :by Shreerang Pande

Bacterial DNA  replication and segregation: Movie by Debarshi Mitra.


The blue particles are a ring polymer confined in a cylinder. The chain models model a bacterial DNA. It makes a copy of itself (replication) as time progresses. Thereby, the pink monomers gets added to form an additional red ring polymer within the cylinder as replication progresses.

Note that the cylinder ( the cylindrical bacterial cell wall) increases in length to double its length without changing its width. At the end of the movie, you see that  the two chains SPONTANEOUSLY  segregate into 2 parts of the the cylinder. The cell is now ready to divide. We also see the ter-transition at around 45 seconds into the movie.


Interestingly, the BACTERIAL E.coli cell uses physics, i.e. entropic repulsion between the two ring polymers to segregate the two DNAs (mother and daughter) into two parts of the cell, so that cell division can proceed once a DNA has replicated.

-- Higher organisms like human have a complex machinery to do the same, but we are discovering that primitive organisms like the E.coli bacteria use principles of physics to achieve the same !!!!


-- Moreover, (Some) Bacteria use ENTROPY to also organize  DNA within the living cell !!

4. How does Stiffness gradient along body column of hydra organism play a crucial role in its ability to perform somersaults? (completed by Devanshu Sinha)

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  1.   One of the first organisms in evolution to develop locomotion ability (700 million years ago).

  2.   Hydra (5mm) has stiffness gradient along body column, as measured in AFM experiments.

  3.   How does this stiffness gradient help in Hydra locomotion??

  4.   Could give a clue how organisms evolved to move around on surfaces.

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5. How can one obtain directed angle dependent interaction potentials starting out from spherically symmetric potentials? : (completed by Alex Abraham)

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Self-assembly of short aggregates to long linear polymer chains  at higher densities using sphero-symmetric potentials

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6. Why do self-assembling linear polymers form shear bands? What are shear bands?

(Open PhD position): work started by Devanshu.

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You see in the video that after shearing the fluid for some time, the fluid breaks up into 2 regions with 2 different flow rates (2 strain rates). Why does that happen? What is microscopically different  in the 2 regions  so that you see the appearance of 2 flow regions?

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7. How do macromolecules self-assemble themselves into exactly the same size and shape in virus capsid ? : An investigation of a simpler alternative system. (open position)

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8. How can we INDUCE LONG RANGE ATTRACTIONS (at the micron length scales) TO SELF- EMERGE between 2 particles enmeshed in a polymer gel network, by switching on  SHORT-RANGE hydrophobic attractions at  nano-meter length scales?  

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8b.      Effective ATTRACTION can be induced between adjacent micron sized colloids in a chain of colloidal particles, so that the entire chain shrinks. 

BUT WHY  WOULD THE SHRINKING CHAIN FORM SELF EMERGENT HELICES ?  ACS-Nano -2021,

Experiments by Guruswamy group-IITB

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MOVIE (created by Debarshi) : the red beads are monomers of a stiff colloidal polymer.

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SLOWER MOVIE SO THAT YOU BETTER FOLLOW THE HELIX FORMATION.

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HOW DO YOU SEW UP MICRON SIZED PARTICLES  TO FORM A CHAIN ?

Experiments by : K. Guruswamy (IITB), Bipul Biswas (NCL, currently in UMass, Amherst.)

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A polymer mesh is adsorbed on  the surface of spherical colloids.  These are then lined up  by inducing  dipolar attractions by placing them in an electric field.  Then the polymer mesh on  the surface of different colloids are cross-linked with each other by adding a cross-linker to the solution.

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Finally,  micron sized colloids are trapped in a inter-connected mesh of polymers and behave like a semi-flexible polymer constituted  of giant colloidal-monomers: PICS above.

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8c.  Emergent (transient) helical structures in stiff chain with REPULSIVE forces with particles and without torsional potentials:  D. Mitra

Published in J.Phys:Condens.Matter.

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9. A  spongy material  made up of hard rigid spherical nano-particles  with large pores which is highly compressible  but spring back to its original shape.  The particles are enmeshed in a polymer gel which makes it deformable but also elasticity to give shape to the scaffold.

A multiscale modeling challenge : A nm thick polymer mesh surround 22 nm nano-particles
to form nano-composite walls of thickness of 1 micron, and dimentions of 10-50 microns which surround open void of size 100 microns to make a sponge of size 1cm. All length  contribute to the combined  elastic response of the composite material.

How does one do it ? Which degrees of freedom to coarse-grain out and how ?



MOVIE BY ANISH SUKUMARAN (IITB B Tech student).

 
Following the deformation of a single void.


       The junctions   surrounding the voids are made of hard nano-particles trapped in a polymer mesh. The polymer mesh gives the scaffold soft and deformable. 95% of the scaffold is Nano-P which are  hard particles of materials like SiO2. If the scaffold were fully made up of solid material like Calcium phosphate or SiO2, it would be brittle. The large voids make the substance very light.

 A 3 minute talk by Anish Sukumar on the system.














Box with 27 CONNECTED VOIDS.
                    ONLY HALF OF THE  BOX IS SHOWN.The colour gradient along z-direction helps the viewer distinguish different  particle layers along z & has no other significance.

-  IN COLLABORATION with K. GURUSWAMY  (IITB)  and N. BACHHAR (IIT-Jodhpur)

--  Extension of project by Somesh Kurhatti:  Replace the spherical particles in the polymer mesh by ellipsoidal nano-particles, that is expected to significantly alter its elastic properties.

Future Plans:

Questions for future students: How  can this study be extended to understand mechanical properties of  Bones or Shells (of marine living organisms) and correlate it to their microscopic structure?   Basic info about porous bones.


--How can one make the system harder while maintaining the flexibility (remain non-brittle) ?

--  There should already quite some literature about mechanics and structures of (human) bones. Bird bones have large pores to make them light. Spinal cord fluids, which form a cushion between bones, have self assembling filaments floating in a fluid medium which give it the necessary elastic + flow properties.

--  How are Shells different from Bones ?  Shell of a turtle vs oyster shell vs clam shells vs...dont know what. How are these shell properties optimized for different organisms?


-- A collection of articles and basic information about micro-structure of BONES AND SHELLS
: the webpage  created by Aparna Jayaraj and Nishanga P: IISER Pune students.

--  Does this help ?  https://www.nio.org/profile/1219/dr-narsinh-thakur

--  Finally the question is how does nature manipulate micro structure to obtain the required stiffness/softness/brittleness/ductility/compressive strength/tensile strength/flexibility..? Whatever the organism needs to survive it's ecological niche

 
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10. How does dynamics of  polymers get modified when confined between fluctuating surfaces (Membranes)? : Multiscale Simulations (MD +MPCD)  with hydrodynamics.

OTHER INTERESTS:

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(a) Microfluidics    (b) Active matter

(c) Phase transitions and statistical physics  of  Soft matter systems

(d) Computational techniques

 

  Shear of (Star-) polymers using multi-scale simulations : Molecular dynamics + MPCD:

  MOVIES:

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1. At 5 star polymers at low shear rates

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2. Only 5 star polymers shown at high shear rates

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3. Only 27 polymers shown at high shear rates.

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4,  Star polymer In extensional flow

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5. Electrophoresis of Charged colloids-1

 

6. Electrophoresis of Charged colloids-2 (higher Electric field)

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