NILAY K ROY

412 Langley Road, Apt 7

Newton, MA 02459

(508) 226 2261

nilayr@yahoo.com

 

Click here for a pdf version.

 

EDUCATION

 

The University of Georgia, Center for Simulational Physics, Department of Physics and Astronomy, Athens, GA  2001

PhD Simulational/Computational Physics

·         Title of Dissertation: Monte Carlo studies of phase transitions in lattice models.

·         Research Advisor: Dr. David P. Landau, Director and Professor, Center for Simulational Physics.

·         Admitted to PhD Program: Sep 1993; Graduated with PhD: May 2001

 

The University of Georgia Department of Computer Science, Athens, GA 2000

MS Computer Science

·         Title of Thesis: Designing Polymer Blends using Neural Networks, Genetic Algorithms, Markov Chains, and an Intelligent Information Manager.

·         Research Advisor: Dr. Walter D. Potter, Professor, Computer Science Department and Artificial Intelligence Center.

·         Admitted to MS program: Jan 1999; Graduated with MS: Dec 2000

·         MS Computer Science done concurrently with Ph.D Physics

 

University of Bombay (Mumbai), Department of Physics, Bombay (Mumbai), India 1992

MPhil Polymer Physics

 

University of Bombay (Mumbai), Bombay (Mumbai), India 1990

BEd

 

University Institute, Department of Physics (Center of Advanced Studies), Bombay (Mumbai) (Department) of Chemical Technology, Bombay (Mumbai), India 1988

MSc Polymer Physics

 

University of Bombay (Mumbai), Bombay (Mumbai), India  1984

BSc Physics/Electronics

 

SPECIALIZATION

 

·         Computational

o   Algorithms/Artificial Intelligence: Neural Networks, Genetic Algorithms, Markov Chains, Metropolis Monte-Carlo, Molecular/Spin Dynamics, Image Processing, Machine Vision, Polymer Modeling, Intelligent Information Managers.

o   Polymer and Polymer Blend Thermodynamics and Modeling.

o   Periodic Bond Chain and related models to simulate forms and habits of molecular crystals.

o   Targeted Molecular Dynamics (TMD) to study molecular crystal transformation mechanisms.

o   Inorganic / Organic / Molecular / Pharmaceutical Crystal Growth, Engineering, Structure Determination, Stabilization, Modeling and Polymorphism / Polytypism.

 

 

·         Programming

o   Development Tools/Languages: Visual C++, Java/NetBeans IDE, MPICH, LAM-MPI, OpenMP, PUB-BSP, MASM, Greenleaf Libraries, Prolog/LISP, OpenGL, DDD, Vampir Pallas/TotalView Parallel Debugger.

·         Operating Systems

o   Windows / UNIX / Linux.

·         Instrumentation:

o   DTA/TGA, DSC, rheovibron, rheogoniometer, instron, X-ray diffraction (WAXS, SAXS, Kratky and Weisenberg Single Crystal Camera), SEM/TEM, GC/HPLC, IR/VIS/UV spectrophotometers, FTIR, laser interferometry, plasma irradiation and fluorescence spectrophotometry.

·         Experimental:

o   Polymerization techniques, injection and reaction injection moulding, polymer testing, polymer blend systems (thermodynamics, blend production, IPNs, random and block copolymerization, and ionomeric membranes), liquid crystals and polymer liquid crystals.

o   Growing and characterizing molecular single crystals of proteins, enzymes and amino acids.

 

DETAILS OF SPECIAL SKILLS

 

·         Machine Vision: Have an excellent background in Image Processing and Machine Vision. These include: Thresholding, Noise, Filters, Edge Detection and Enhancement, Orientation, Textures, 3-D imaging.

·         Neural Networks: Have written several Neural Network programs ranging from simple multi-layer back-propagation networks, Hopfield networks, to advanced specialized self-associating networks like Kohonen networks.

·         Genetic Algorithms: Have implemented a high-converge scheme to design Polymer Blends using genetic algorithms and Markov chains. Results published in Applied Intelligence Journal.

·         Parallel Programming: Using LAM-MPI have designed a new technique for adaptive resource management for parallel computing. The results are published in the IEEE Proceedings Journal and were presented in a conference at MIT, Cambridge. Besides this have used extensively the following: MPICH, MPE, Jumpshot, Upshot, OpenMP, PUB-BSP, and PVM. Have considerable experience in mixed level programming using OpenMP and MPI. Have used various parallel debugging and optimizing techniques via trace files, and commercial packages like Vampir Pallas, DDD. Have ported and optimized a wide variety of codes for parallel applications from the Princeton Oceanographic Model, X-Ray crystal structure calculation programs, and Fluid Dynamics programs. Have also written a cluster monitoring and statistical analysis software package for computer clusters running LINUX / UNIX / Windows NT.

·         3-D Graphics / Visualization: Have experience with Direct X, WinG, OpenGL, and Mesa libraries for graphic visualization of simulations both in real time and as an analysis tool.

·         Monte-Carlo / Molecular Dynamics: Have excellent background in Classical and Quantum Monte-Carlo, Low and High temperature series and cumulant expansions, molecular / spin dynamics techniques, Amber, Gromos, Merck and CHARMM force fields.

·         Experimental / Instrumentation: Have extensive experience in all areas of polymer / polymer blend analyses, testing and characterization, synthesis and design. Have used various instrumentation techniques ranging from XRD, spectrophotometers and interferometers to flow and thermal analyzers.

 

 

 

PROFESSIONAL EMPLOYMENT

 

Harvard University, Faculty of Arts and Sciences IT Department, Cambridge, MA Sep 2008 – Nov 2008

Research Computing Associate

·         Cluster administration, help desk, data backups with Lustre file system.

 

Brandeis University, Rosenstiel Basic Medical Sciences Research Center, Waltham, MA May 2007 – Sep2008

Postdoctoral Research Fellow

·         Wrote an installation package using Autotools (Automake/Autoconf) for Signature, an EM program developed at the center.

·         Wrote an MRC viewer. (http://www.webng.com/nilayr/MRC_Viewer.zip)

·         Wrote an image manipulation software package that reads TIFF, BMP and JPEG files, splits and converts TILE oriented TIFF images from multiple negatives scanned from the Zeiss SCAI Scanner to regular TIFF or MRC files, implements an OD table for images scanned from the NIKON supercool scan 9000 ED scanner, and has a particle picker. (http://www.webng.com/nilayr/TIFFSampler.zip)

·         Wrote a software package that uses the CHARMM force field and the electron density from EM images to create atomistic models by fitting the electron density from the EM images to a similar electron density from the atomic model using energetic considerations. The software allows easy building of the amino-acids with energy calculations being done on the fly while viewing both the EM image and the model electron densities.

 

Brandeis University, Department of Chemistry, Waltham, MA, Mar 2005 - Apr 2007

Postdoctoral Research Fellow

·         Computational simulations of large molecular systems (>106 atoms) to determine gating mechanism in channel proteins.

·         Implemented several new algorithms for computations of interactions including the Fast Mulitpole Method and the Boundary Element Method.

·         Implemented the above algorithms with the CHARMM force field to develop new ways to model and study gating in ion channels.

·         Did large scale simulations using the above methods and further developed and refined these methods to both model the gating and elucidate the open and closed states of ion channel proteins via computational methods.

·         A static version of the Ion Channel Simulator that implements the CHARMM force field. (http://www.webng.com/nilayr/NKR_ION_CHANNEL_SIMULATION.zip)

 

Carnegie Mellon University, Department of Physics, Pittsburgh, PA Oct 2003 - Feb 2005

Postdoctoral Research Associate

·         Experimental, Theoretical and Simulational study of polymorphism in pharmaceutical crystals.

·         Experimental: Grew large single crystals of l-glutamic acid in both its polymorphic forms, and obtained mixed crystals showing the transformation. Studied the crystals using standard microscopy, X-ray single crystal and 3D X-ray methods. Also studied the polymorphs of Insulin. Designed and fabricated an 11mm thick variable temperature cell (4 - 600OK) to study the polymorphic transitions in microscopy and XRD for mainly in-situ work.

·         Theoretical: Applied theories of nucleation and crystal growth to determine the phase space (temperature, buffer type and pH, super saturation, and seeding) to work in to obtain large single crystals, and how to stabilize the different polymorphs in solution and during and after growth.

·         Simulational: Using the periodic bond chain model and targeted molecular dynamics studied the mechanism of the transformations and modeling the different forms and habits in various molecular crystals.

 

IntelliSol Consulting Inc., Toronto, Ontario, Canada Jun 2002 - Sep 2003

Chief Consulting Engineer

·         Responsibilities and Accomplishments:

·         Providing high performance computing solutions to a variety from clients ranging from aircraft/automobile design, finance and forecasting, visualization, machine vision, robotics, pharmaceutical and bio-informatics to material and drug design.

 

Microway Inc., Plymouth, MA Jan 2001 – May 2002

Senior Scientist

Responsibilities and Accomplishments:

·         Designed and implemented using C++, MFC and MASM / Greenleaf Libraries controller codes and a GUI for master and slave nodes for monitoring of the I2C bus on motherboards for computers connected via a 8051/RS485 card interface.

·         To monitor parameters like CPU temperatures, fan speed, voltages in a cluster of computers using the I2C bus created a database program for the master that stored node level information and generated statistical fluctuation information enabling identification of failing nodes and pinpointing the problem on the motherboard.

·         Created and refined a Part List / Net List file comparator program for comparing files from programs like CAM 350, PADS, ORCAD and SPECTRA to provide detail Part level and Net level comparisons, as well as convert from one file format to another. This cut motherboard rerouting and development time by enabling easy portability of various file systems between programs, and allowed for easy verification of circuitry with controls.

·         Invented an adaptive resource management software package for computer clusters running MPI, OpenMP or PVM under any OS. This was presented in an international IEEE supercomputing and networking conference at MIT, Cambridge, USA and was published in their proceedings journal.

·         Overcame the time synchronization problem for windows based clusters by writing a program in VB which when run on the master achieved accurate time synchronization of the entire cluster with atomic time. This is critical for parallel file I/O, check pointing and backtracking of parallel programs.

·         Using ER Studio normalized and then created an Intelligent Sales Quoting System in Microsoft Access / VBA that allowed for easy and almost automatic creation of quotes for computer clusters for a wide variety of configurations and OS’s with instant verification of availability and delivery time based on inventory and back order workload and configuration corrections/suggestions if not feasible.

·         Wrote a 20000+ line cluster monitoring and statistical analysis software package in PERL/Tcl-Tk for monitoring and debugging failing nodes in a cluster of computers with remote monitoring via TCP/IP and a web based interface.

·         Have written over 15 application notes and white papers. (http://www.microway.com/papers/appnotes/Microway_Working_Note_Index.html) Topics include system and kernel level programming, distributed computing, parallel programming paradigms.

·         Interfaced with potential customers by running benchmarks, parallelizing existing code, and optimizing their existing parallel programs.

·         Did extensive debugging of clients serial and parallel code using DDD, Visual Studio, Vampir Pallas / TotalView debugger for parallel applications.

Platforms: UNIX, LINUX, Windows NT/2000/9x/Server/Advanced Server/Datacenter Server, Visual Studio 6.0 Enterprise, Forte for Java Enterprise / NetBeans IDE, ERStudio.

 

Rashesh Chem. & Pharm. Pvt. Ltd., Bombay, India.  Feb 1993-Aug 1993

Project Manager

·         Designed and tested a toluene-sulphonamide resin pilot plant.

·         Set up a product testing laboratory.

 

Atlas Metal Processors Pvt. Ltd., Madras, India. Oct 1990-Jan 1993

Systems Engineer

Responsibilities and Accomplishments:

·         Was responsible for process control and monitoring of their sheet steel production factories and supervised a team of engineers, technicians and workers.

·         Appointed the lead project specialist for an automation project being undertaken for their sheet steel production factories During this time in Basic with dBase I wrote device drivers for various sensor and control devices, designed and set up a GUI to monitor, control and display graphically in real time various system and control parameters, and created a database for the storing of process information with an easy query interface for generating process reports thereby simplifying on line process monitoring and process control.

·         On successful completion of this project was awarded a citation and a cash bonus from the Managing Director of the company.

Platforms: Basic, dBase, MSDos.

 

Indian Institute of Technology, Bombay, India. Jun 1989-Oct 1990

Junior Research Fellow

·         Worked on NBS sponsored project "Thermodynamics of aqueous solutions".

 

Bharat Bijlee Limited, Bombay, India. May 1985-Sep 1987

Junior Supervisor

 

PhD Computational/Simulational Physics Research Work

·         Using C++ (UNIX/LINUX and NT) wrote simulation programs for the Bond Fluctuation Model and the Potts Model, with 3-D visualization using OpenGL Libraries that implemented various Metropolis Monte-Carlo based cluster algorithms.

 

MS Computer Science Research and Course Work

·         Wrote a Neural Network, Genetic Algorithm, Markov Chain simulation program in Visual C++ for modeling polymer blends and an intelligent information manager for polymer blend design based on ASP’s and a rules database.

·         As part of the course work did a project that utilized a distributed geographic database of the city of Athens (GA, USA), and PVM. The database was on several UNIX/Windows machines. Using distributed SQL queries with PVM and parallel sort merge algorithms road maps could be obtained between points (in the city of Athens) by directly typing in street names.

·         Using Borland Delphi 3.0 Client / Server Suite wrote a multiple fault diagnosis program based on a genetic algorithm as part of the course work.

·         Did an extensive project on machine vision and handwriting recognition using Neural Networks.

 

 

Teaching Experience Sep 1993 - Dec 2001

Teaching Assistantship

·         Was instructor for various physics labs and CS2610 computer science discrete math course at The University of Georgia.

 

PUBLICATIONS

 

·         K. Kalkar and N. K. Roy, “Dynamic Mechanical Properties of Bisphenol –A Polycarbonate/Poly(p-t-butylphenol formaldehyde) Blends”, Polymer Science Contemporary Themes, Volume II, p894, 1992, Editor S Sivaram, Tata McGraw-Hill Publishing Company Limited, New Delhi.

·         K. Kalkar and N. K. Roy, “Thermal and Dynamic Mechanical Properties of Polycarbonate/Poly(p-t-butylphenol formaldehyde) blend films”, European Polymer Journal, Volume 29, No.10, p1391, 1993.

·         N. K. Roy, “Real Time Resource Management and Adaptive Parallel Programming for a Cluster of Computers: A comparison of different approaches in a computationally intensive environment”, Proceedings of IEEE Computer Society, IEEE International Symposium on Network Computing and Applications, October 2001, p216-226.

·         N. K. Roy, W. D. Potter and D. P. Landau, “Designing Polymer Blends using Neural Networks, Genetic Algorithms, and Markov Chains”, Applied Intelligence, 20 (3), p215-229, May - June, 2004.

·         N. K. Roy, W. D. Potter and D. P. Landau, “Polymer property prediction and optimization using neural networks”, IEEE Transactions on Neural Networks, 17 (4), p1001-1014, July-August, 2006.

 

TALKS

 

·         N. K. Roy, “Phase transitions in the q=5 state Potts model in a uniform external magnetic field”, Centennial APS March Meeting, Atlanta, GA, USA, 1999.

·         N. K. Roy, “Designing Polymer Blends using Neural Networks, Genetic Algorithms, and Markov Chains”, APS April Meeting, Los Angeles, CA, USA,  2000.

·         N. K. Roy, “Phase transitions in a grafted polymer using the Bond Fluctuation Model”, APS March Meeting, Seattle, WA, USA, 2001.

 

POSTERS

 

·         N.K. Roy and Peter Jordan, Explicit and Semi-explicit atomistic level studies of the KCSA channel in a lipid bilayer and solvent environment, 2006 Biophysical Society Meeting, Salt Lake City, UT, USA, February, 2006.

·         N.K. Roy and Peter Jordan, Semi-explicit nanosecond simulations of a voltage gated potassium channel using a novel boundary element method, Gordon Research Conference on Ion Channels, Tilton, NH, USA, July 9-14, 2006.

 

JOURNAL ARTICLE REVIEWER

 

·         POLYMER

·         Chemical Engineering Communications

 

 

 

 

 

ADDENDUM

 

·         Can read and write French having studied it till 12th grade.

·         Completed a course on “Polymorph Screening – Techniques and Applications” held in Stamford, CT, USA (Oct 15-17, 2003) by “ASSA International Inc.” (http://www.assainternational.com)

·         Wrote a MDI based multi-threaded fast and lightweight web browser in C++. (http://www.softpedia.com/get/Internet/Browsers/N-K-Roy-Browser.shtml)

 

COLLABORATIONS

 

·         Aay-Kay Plastic Industries, Bombay, India: Routine testing of products for quality control.

·         Engineered Polymers (India) Pvt. Ltd., Bombay, India: Set up reaction injection molding processes for different polyamides and polyurethanes.

·         Gemini Metal Works, Madras, India: Developed different thermoplastic insulation for stainless steel cookware.