Group Members

Present Group Members

Angan Sengupta

Aniket Deb 

M. Harini (Guide: Dr. Yamuna Rani, IICT Hyderabad)

Rupak Kumar 

Sanjib Sikder

Shanu Jain 

Spandana  Ramisetty 

Sudheer  Gondu 

Tamaghna Chakraborti

Group Alumni

Anish Desouza

Ankur Varshney

Pratik Behera

Punit Rathi

D. Krishna Mohan (with co-guide)

Parul Sahu (with co-guide)

Mrugendra Kamtikar

Gunja Rajesh Pandav (with co-guide)

Manas Kumar Mandal

Vibhu Arora

Piyush Maheshwari

Atul Kumar

Sumint Singh Trivedia

Publications

1. M. Harini; Adhikari, Jhumpa and K. Yamuna Rani, A Review on Property Estimation Methods and Computational Schemes for Rational Solvent Design: A Focus on Pharmaceuticals Industrial & Engineering Chemistry Research (2013) 52 (21), 6869–6893
2. Rathi, Punit; Sikder, Sanjib and Jhumpa Adhikari, Structural characterization of III-V zinc blende compound semiconductors using Monte Carlo simulations Computational Materials Science (2012) 65, 122-126
3. Adhikari, Jhumpa, Thermodynamic modelling of miscibility in (InAs)x(GaAs)1-x solid solutions . Phase Transitions (Accepted, 2012)
4. Book Chapter : Jhumpa Adhikari, "Design of Compound Semiconductor Alloys Using Molecular Simulations" in Molecular Modeling for the Design of Novel Performance Chemicals and Materials, Editor: Beena Rai, CRC Press (2012) ISBN: 978-1439840788
5. Sikder, Sanjib; Rathi, Punit and Jhumpa Adhikari, Molecular simulation predictions of miscibility characteristics and critical exponents in compound semiconductors Journal Of Crystal Growth (2011) 324 (1), 284-289
6. Sikder, Sanjib; Rathi, Punit and Jhumpa Adhikari, Structural characterization of pseudo-binary semiconducting alloys using molecular simulations Molecular Physics (2010) 108 (24), 3405-3415
7. Adhikari, Jhumpa, Miscibility of InxGa1-xAs alloys: a study using atomistic simulations. Molecular Physics (2009) 107 (16), 1641-1648
8. Adhikari, Jhumpa, Molecular simulation study of the microstructure of InxGa1-xAs alloys: Comparison between Valence Force Field and Tersoff potential models. Computational Materials Science (2008) 43 (4), 616-622
9. Adhikari, Jhumpa and A. Kumar, Study of structural and thermodynamic properties of GaAs and InAs using Monte Carlo simulations. Molecular Simulation (2007), 33(8), 623-628
10. Kwak, S. K.; Singh J. K.and Jhumpa Adhikari, Molecular Simulation Study of Vapor-Liquid Equilibrium of Morse Fluids. Chemical Product and Process Modeling, Berkeley Press (2007), 2(3), Article 8
11. Singh, J. K.; Adhikari, Jhumpa and S. K. Kwak, Interfacial properties of Morse fluids. Molecular Physics (2007) 105(8), 981-987
12. Singh, J. K.; Adhikari, Jhumpa and S. K.Kwak, Vapor–liquid phase coexistence curves for Morse fluids. Fluid Phase Equilibria (2006), 248(1), 1-6
13. Adhikari, Jhumpa and D.A.Kofke,Molecular simulation study of miscibility of ternary and quaternary semiconductor alloys. Journal of Applied Physics (2004), 95(11), 6129-6136
14. Adhikari, Jhumpa and D.A.Kofke, Molecular Simulation Study of Miscibility in InGaN Ternary Alloys. Journal of Applied Physics (2004), 95(8), 4500-4502
15. Lu, Nandou; Adhikari, Jhumpa and D.A.Kofke, Variational Formula for the Free Energy Based on Incomplete Sampling in a Molecular Simulation.Physical Review E: Statistical, Nonlinear, and Soft Matter Physics (2003), 68, 026122 (7 pgs)
16. Adhikari, Jhumpa and D.A.Kofke, Monte Carlo and cell-model calculations for the solid-fluid phase behaviour of the triangle-well model. Molecular Physics (2002), 100(10) 1543-1550

Research

Research Interests

• Molecular Simulation
• Molecular and Statistical Thermodynamics

Overview

Molecular Simulations techniques such as molecular dynamics and Monte Carlo simulations are used in the development of new methods for determination of free energies and phase equilibria, especially as applied to solids and alloys.Simulation of solids provide an unique challenge because of the high densities involved which preclude use of any of the well established insertion/deletion methods used in the fluid phases. This provides an opportunity for the development of new methods to successfully measure the free energy of the solids and to improve the efficiency of the techniques used. Inter-atomic potential models are developed and investigated for applications of molecular simulation techniques to study solid fluid phase equilibria. Molecular simulation techniques are applied to determine the solubility diagrams for solid solutions, such as ternary and quaternary compound semiconductor alloys, and also to predict the structural properties, local composition and thermophysical properties of the above mentioned alloys. Compound semiconductor alloys have properties which are usefulfor the manufacture of optoelectronic devices. The application and continued development of java package called "etomica" (DAK group, University at Buffalo) for molecular simulations.

Design of compound semiconductor alloys using molecular simulation

Compound semiconductors alloys are used in the manufacture of optoelectronic devices, such as high brightness Light Emitting Diodes and semiconductor laser diodes. The cost of development of these ternary and quaternary alloys into a marketable devices using only experimental research is very high. Using computer simulations in conjunction with experiments lower the costs involved in researching these alloys as simulations can be used to reduce the alternatives to the point where only the useful alloys can be subjected to experiments.

Molecular Simulation determination of vapour-liquid equilibria and surface tension of metals

Property prediction for metals at extreme conditions (high temperatures and pressures) is difficult using experiments and often give a wide range of values. The behaviour of metals under these conditions is interesting as metals often show morphologies which are not as observed at room conditions. Molecular simulations using empirical potential energy functions model the interactions between the constituent species in the metal and predict property values that are consistent with these inter-particular forces while providing explanation of the underlying molecular mechanism.

Computational Facilities

HPC cluster with 3.2 GHz Intel Xeon Processors

Current Research

Thermodynamic property prediction of nano-confined fluids using molecular simulations

Fluids confined in nanoporous materials have properties which are different from bulk phase. These properties enable the novel applications of these materials. Experiments at dimensions of the order of nanometers are difficult. This project involves the characterization and understanding of properties such as phase segregation, adsorption, etc., in pores of nanometer dimensions using molecular simulation techniques

Multi-scale simulation of III-V compound semiconductors

This project envisages development of a novel multi-scale simulation scheme to design the III-V compound semiconductor alloys, which are used or have the potential to be used, in several applications such as devices for optical data-storage, fibre-optics communications, infra-red cameras, imaging sensors, specialty lasers and low power, high brightness lighting.

Molecular Simulation study of the miscibility behaviour and microstructure of compound semiconductor alloys

The work under this topic envisions a molecular simulation study of the miscibility behaviour and the microstructure in compound semiconductor alloys. The Tersoff potential model is the interatomic interaction potential for the InxGa1-xAs alloy system, which is selected as a representative example of these alloys. The alloy will be modelled for a range of compositions (considering x from zero to unity) and temperature from 100 K to the measured upper critical solution temperature. The bulk phase and thin films are both considered in the study. The microstructure is characterized by properties such as lattice constant and bond length, which are useful to measure as a way to connect to experiment and thereby, validate the model. The local composition as predicted by simulations can help in predicting the effect of microphase segregation that is difficult to quantify experimentally. The existence of even small microphases can have a disproportionate effect on the optoelectronic properties of these alloys. Monte Carlo simulations in the isothermal-isobaric semigrand ensemble are used for simulation purposes. InxGa1-xAs has been chosen due to its special properties, which enable its extensive use in fibre optic communications. Though this work is modelling the InxGa1-xAs alloy system, it can be easily be extended to other III-V and II-VI compound semiconductor alloys.

Teaching

Courses Taught

Course web pages are available on moodle

CL 607 Advanced Thermodynamics

CL 260 Molecular And Statistical Thermodynamics

CL 465 Stochastic Processes

CL 316 Computational Lab II

CL 251 Thermodynamics I

iGEM 2009 Updates

The updates for iGEM 2009 are presented here which are included after the deadline of wikifreeze on iGEM 2--9 website.

Conclusions of the project:

We characterized a phenotypic property of a cell (growth) with the help of synthetic genetic circuits. We proved that the specific growth rate on lactose was optimized in the mutant strain containing multiple feedbacks. The noise or variance associated with the protein expression of a MIMO strain was comparatively lower than that of Open loop strain containing zero feedbacks. We were successful in quantifying the gene expression using synthetic networks and correlate the intrinsic noise at the expression level to the phenotypic response of growth. Simulation and control analysis proved conclusively the advantages of multiple feedback to regulate inherent noise in the system. It is therefore, no surprise, that nature has evolved such a multiple feedback design which is observed in systems ranging from bacteria to humans.

Brownian Dynamics using MMTK

These are a collection of lectures on the extending the Molecular Modelling ToolKit (MMTK) (which is a generic Python library/package for molecular dynamics) to perform Brownian Dynamics Simulations. The lectures are organised in various modules:

1. Introduction to Python and Object Oriented Programming.
2. Simple scripting to perform basic MD and BD

These lectures were delivered and recorded in Monash University during Nov-Dec 2009. I thank the author of MMTK Dr Konrad Hinsen, for providing useful comments and insights in preparing these lecture slides, and Dr J Ravi Prakash, for providing the support to carry out this work.

CL254 Links

Here are some links useful to students who have not yet registered or who are not yet able to access the moodle login. Please use the moodle login ASAP, as the contents here will not be updated regularly.

Details of Research Projects

Liposome, Microfluidics

Meeting Schedule

Please consult the calendar below to find my availability, for a meeting.

Polymer Rheology

Presentation file and Audio Lecture given in SERC school on Rheology of Complex Fluids in IIT Madras, Chennai Jan 2010.

Polymer Simulation Companion: An Introduction to Brownian Dynamics

Notes and program source codes for lecture delivered in SERC School on Molecular Simulations, IISc Bangalore May 2009, are provided here for download.

Skills for Scientific Communication

Here we collect a set of lectures delivered in Communication Skills course, part of which is conducted by the department. An all round approach has been followed, starting from introduction to the scientific methodology, and up to some details in actually using a software's assistance for communication.

Curriculum Vitae

Detailed CV of Rajdip Bandyopadhyaya as of 2011

Instruments

Instrument	Status	Contact	Ph. No.
Bacteriological Incubator	Working	Sopan	4237
Sterio Zoom Microscope	Working	Rajkumar	4225
Function Generator	Working	Priya	4237
Oven	Working	----	-----
Rotary Evaporator	Working	Yogita	4206
Optical Microscope	Working	Priya	4237
DLS	Working	Priya	4237
Laminar Hood	Working	Sopan	4237

Small instruments

Research Interest

• Fluid Mechanics and Electrohydrodynamics
• Nanoparticle synthesis
• Soft condensed and colloidal physics