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2018

GIAN @ SCIS : Workshop Series, July 30 - August 04, 2018

 

SYNTHETIC ANALOG CIRCUIT DESIGN IN LIVING CELLS

By : Professor Rahul Sarpeshkar is currently the Thomas E. Kurtz Professor at Dartmouth College and a Professor of Engineering, Microbiology and Immunology, Physics, and Physiology and Neurobiology. His longstanding and frequent work in analog and biological computation, his book, Ultra Low Power Bioelectronics: Fundamentals, Biomedical Applications, and Bio-inspired Systems, and his most recent publications have pioneered the pioneered the field of Analog Synthetic Biology. This content will form the basis of the course.
His unique interdisciplinary research creates both wet DNA-protein and dry electronic analog circuits, many of which have achieved world records. He holds over 36 awarded patents and has authored more than 127 publications, including one that was featured on the cover of Nature.
He has won several awards for his interdisciplinary work including the NSF Career award, the ONR Young Investigator award, and the Packard Fellow award given to outstanding faculty. His work on a glucose fuel cell for medical implants was featured by BBC Radio, the Economist, and listed among Scientific American’s top ten breakthroughs of 2012. Professor Sarpeshkar obtained Bachelor’s degrees in Electrical Engineering and Physics at MIT. After completing his PhD at CalTech, he joined Bell Labs as a physics member of technical staff in their department of biological computation. Before joining Dartmouth, he was a tenured professor at MIT for several years.

Overview

Living cells use DNA-RNA-protein circuits to perform sensing, actuating, computing, and control functions with amazing energy and part-count efficiency. They use noisy and unreliable parts to perform reliable computation with probabilistic digital and collective analog strategies. The complexity of computation within the ~30,000-node nonlinear, stochastic, feedback dynamical system in a single cell is so staggering that our attempts to engineer cells (synthetic biology) or to understand their function and malfunction (systems biology and medicine) are still in their infancy after decades of research. The treatment of several diseases from cholera to cancer would be revolutionized if we had a principled way to design and analyze circuits in living cells.
Based on the astounding similarities between the mathematical equations that govern biochemical reaction flux and electron transport in subthreshold transistors, both of which obey the Boltzmann laws of thermodynamics, it is possible to map analog electronic circuits to analog bio-molecular circuits and vice versa in a principled fashion. Digital circuits comprise a special case and are automatically included as well. Founded on these similarities, this course will introduce the basics of a cytomorphic approach for designing circuits in cells based on analog transistor circuit design.
The course is offered by Prof. Rahul Sarpeshkar, who has pioneered the fields of analog synthetic biology and cytomorphic electronics. His work on analog circuits and analog computaiton has had and continues to have several applications in biotechnology, implantable medical devices, microbiology and immunology, and bio-inspired and ultra-energy-efficient systems.

Objectives

I. This course will introduce :
[1] Fundamentals of Feedback Systems.
[2] Subthreshold transistor physics including the fundamentals of noise, linear, and nonlinear operation.
[3] The Representation of Biological Pathways and Networks with Electronic Circuit Schematics.
[4] Synthetic Biological Circuit Design Using Analog Circuit Design.
II. To build an India-centric community which uses integrated skills drawn from electrical engineering, bioengineering, biotechnology, and computational biology.

 

Poster & Schedule

 

Teaching and Learning Methods

Course details
1. Introduction: Circuit Pathways and Networks in Cells. The key ideas behind the cytomorphic mapping. A big-picture view of the course including an outline.
2. Feedback Systems: The linear feedback loop. Feedback loops and circuits. Root-locus techniques in controls system analysis and design. Feedback loops in biology and electronics.
3. Transistors: Metal-oxide-semiconductor (MOS) transistor operation. Weak-inversion, Strong-inversion, Small-signal models.
4. Analog Circuit Representations of Cellular Computation : Analog v/s Digital computing. Analog Synthetic Biology. Schematics for DNA-protein computation in cells including analog, logic, and analogic functions.
5. Thermodynamic Circuits in Electronics and Living Cells : Electronic analogies of chemical reactions. Log-domain current-mode models of chemical reactions and molecular networks. Analog circuit models of gene-protein networks.
6. Logarithmic Analog Computation in Living Cells : Design and implementation of synthetic analog circuits in cells. The creation of a bio-molecular slide rule that computes.
7. Synthetic Biology: A unifying view and review using analog circuits : A Review of 17 circuits in Synthetic Biology using the language of analog circuits.
Additional topics to be covered by host faculty will include lectures on Signals and Systems, and on Synthetic and Systems Biology.

Who can attend ?

•Executives, engineers and researchers from manufacturing, service and government organizations including R&D laboratories.
•Students at all levels (BTech/MSc/MTech/PhD) or Faculty from reputed academic institutions and technical institutions.

Registration Fees

JNU M. A. / M. Sc. Students : Free
JNU M.Phil/Ph.D students : ₹ 1000.00
JNU Faculty : ₹ 2000.00
Students of other recognised institutions : ₹ 2000.00
Faculty of other recognised institutions : ₹ 4000.00
Industry, private institutes : ₹ 10000.00
Participants from outside India : ₹ 10000.00

How to apply ?

 

Registration


Formal Registration for those participants who would like recognition from the GIAN program is through that portal at http://www.gian.iitkgp.ac.in
There is a one-time portal user registration charge of Rs 500/-, and thereafter a payment to be made at the portal for the course.


 

However, if the participant is from Delhi, we would be glad to offer a certificate of participation from the School and there would be no charge. Please Register here

 

 
Talk : All the world's Knowledge
Speaker : Carl Malamud an American technologist,
author, and public domain advocate,
known for his foundation Public.Resource.Org
31st May, 2018 at 3:00 pm at Arts & Aesthetics Auditorium, JNU
M&CEC & SCIS is organising Hands-on
Workshop on APPLICATION OF NETWORK THEORY IN SOCIAL SCIENCE
For registration visit https://jnu.ac.in/mcec_register
Date & Time & Place: 26th April, 2018 & 1st May, 2018 - 4:00 pm- 6:00 pm , Seminar Hall, SCIS, JNU
JOURNAL CLUB SEMINAR
Speaker: Prof. G.C. Sharma
A Theoretical Approach for activation of pro- drug by conjugate and its Localization in Cancer Chemotherapy

Speaker: Prof. G.C. Sharma

Date & Time & Place: 19th April, 2018 - 4:00 pm, Seminar Hall, SCIS, JNU
Scientific Talk
Rapid and efficient generation of neural cells from mouse pluripotent stem cells and their successful enrichment

Speaker: Isha Verma
Department of Molecular Reproduction, Development and Genetics
I. I. T. Kanpur
ndian Institute of Science, Bangalore-560012
Date & Time & Place: 9th April, 2018 - 3:00 pm, Seminar Hall, SCIS, JNU
Seminar
Nature’s Laws : Single equation or hierarchical laws?

Speaker: Prof. Mahendra K. Verma
Dept. of Physics
I. I. T. Kanpur
Kanpur 208016, India
Date & Time & Place: 3rd April, 2018 - 3:00 pm, Seminar Hall, SCIS, JNU
School of Computational & Integrative Sciences, JNU
&
Commission for Scientific Technical Terminology
MHRD, Govt. of India

Seminar : GRAPHS, NETWORKS & Application of MATHEMATICS in
Computation, Engineering, Bioinformatics & Social Sciences


Date & Time & Place: 12 March - 14 March, 2018, Audi-II, Convention Centre, JNU
Seminar- Multi-scale Modelling of Large and Complex Biomolecular/Organic Systems
Speaker: Dr. Pierre-André Cazade
Ph.D., Computational Scientist
12 Shreelane Road
Woodhaven
Castletroy, co. Limerick, Ireland
Date & Time: 08th March, 2018 at 2:30 pm, Seminar Room, SCIS
Seminar- Multiscale simulations of amyloid formation and conversion
Speaker: Ulrich H.E. Hansmann
Dept. of Chem. & Biochem., University of Oklahoma
Department of Chemistry and Biochemistry
Norman, OK 73019, USA
Date & Time: 1st March, 2018
Seminar - Network Medicine: From cellular network to human disease
Jointly organised by : School of Computational & Integrative Sciences & School of Biotechnology
Speaker: Amitabh Sharma
Network Medicine Laboratory
Channing Division of Medicine
Harvard Medical School
27 February, 2018
Interaction Meeting with : Nitin S. Baliga, MSc, PhD
Senior Vice President, Director and Professor
Baliga Lab
23rd & 24th February, 2018

workshop on ‘Big Data Analytics & Cloud Technology’
The workshop is jointly conducted by SCIS, SCSS and CIS along with Oracle India.
23rd Feb 2018

Seminar: Utility of extracellular vesicles for linking environmental particulate exposures to toxicological manifestation in humans.
Speaker : Anoop K. Pal
Chief Scientist
Americas Region at Izon Science Boston,USA

Date & Time : 23/01/2018 3:30 pm, Seminar Room, SCIS

Journal Club Seminar: Current problem in Molecular Modelling & Drug Design
Speaker : Dr. Naidu Subbarao
SCIS

Date & Time : 3 pm on 17th January, 2018, Seminar Room, SCIS

Seminar: Random matrix theory for interacting quantum systems
Speaker : Dr. (Ms.) Manan Vyas
Assistant Professor
Fenómenos no lineales y complejidad
Instituto de Ciencias Físicas,
Universidad Nacional Autónoma de México,
Cuernavaca, Morelos, México

Date & Time : 3-4 pm on 3rd January, 2018, Seminar Room, SCIS

Seminar: Utility of extracellular vesicles for linking environmental particulate exposures to toxicological manifestation in humans.
Speaker : Anoop K. Pal
Chief Scientist
Americas Region at Izon Science Boston,USA

Date & Time : 23/01/2018 3:30 pm, Seminar Room, SCIS


2017

Seminar: Physics of sensing and shaping membranes in living cells
Speaker : Prof. Gerhard Hummer

Department of Theoretical Biophysics,
Max Planck Institute of Biophysics, Frankfurt am Main, Germany
Date & Time : 6th December, 2017, 3:30 pm, Seminar Room, SCIS

Workshop:Introduction to computational tools for molecule design
Speaker : Dr Rae Lawrence

Date & Time : 27th November, 2017, 1:45 pm, Seminar Room, SCIS

Seminar: Crowding in heterogeneous media
Speaker : Prof. Allen Minton

Laboratory of Biochemistry and Genetics, Physical Biochemistry Section, National Institute of Diabetes and Digestive and Kidney Diseases,
National Institutes of Health, Bethesda, MD, USA
Date & Time : 24th November, 2017, 3:30 pm, Seminar Room, SCIS

Seminar :Enterpreneurship in Science – What One Needs to Know

Speaker: Sreedhara R. Voleti,
Managing Director, INDRAS Private Limited

Date, Time / Venue : 18/11/17,  011:00 am, Seminar Room, SCIS
Seminar : SYMMETRIES IN NATURE

Speaker: Prof. R. Rajaraman
Emeritus Professor
School of Physical Sciences, JNU.

Date, Time / Venue : 10/11/17 03:30pm -5:30pm Seminar Room, SCIS

Seminar : Advances in Personalized Medicine

Speaker: Prof. G.P.S. Raghava
Indraprastha Institute of Information Technology-Delhi

Date, Time / Venue : 15/11/17,  04:00pm -5:30pm, Seminar Room, SCIS
Seminar : SYMMETRIES IN NATURE

Speaker: Prof. R. Rajaraman
Emeritus Professor
School of Physical Sciences, JNU.

Date, Time / Venue : 10/11/17 03:30pm -5:30pm Seminar Room, SCIS

Seminar : Tryst with Endosomes: A Novel GPCR Activation Paradigm and Therapeutic Opportunities.
Speaker:Dr. Prasenjit Mitra
Dr. Reddy’s Institute of Life Science, Hyderabad
Date, Time / Venue : 31/10/17 10:30 qm, Seminar Room, SCIS

Seminar : Membrane-less organelles and Neurodegenration: The biological underpinnings of neurodegeneration 

Speaker : Prof. Benjamin Wolozin 

Date & Time 13/10/2017, 3:30pm at SCIS Seminar Room


Seminar : Graph Theoretic Concepts in the Study of Biological Networks
Speaker: Dr. S. Arumugham
Director, n-CARDMATH, Adjunct Prof.
Dept. of Computer Science, Ball State University, Muncie, Indiana, USA and Visiting Prof. at Liverpool
University, UK
Date, Time / Venue : 11/10/17 11:00am -12:30pm Seminar Room, SCIS

Symposium : New Trends in Applied Mathematics: From Biology o Finance
Speakers : Dr. Malay Banerjee, Dr. Anindya Chakrabarti, Prof. Sujoy Chakravarty, Dr. Sourish Das, Dr. Sapna Ratan Shah, Mr. Dipyaman Sanyal, Ms. Kiran Sharma
Date, Time / Venue : 11/9/17, 9:00am to 1:00 pm, Seminar Room, SCIS.

Journal Club Semninar : The Role of Time Delay in Biological Systems
Speaker : Shakti Singh Nath Date, Time / Venue : 6/9/17, 3:30pm - 4:30 pm, Seminar Room, SCIS

Talk: "What we can learn from PDB?”
Speakers: Dr. Sameer Velankar, Team Leader PDBe ,EMBL-EBI
and Dr. Aleksandras Gutmanas, NMR Project Leader, EBI
Date, Time / Venue : 31/8/17, 9:00am - 10:00am, Seminar Room SCIS

Talk : “Autophagic Cell Death: The Lethal Side of Autophagy”
Speaker: Dr. Santosh Kumar Dasari
Date, Time / Venue : 31/8/17, 2:00pm - 5:00pm, Seminar Room SCIS

Seminar : Mathematical and Computational Methods in financial markets
Speaker : Dr. Murali Subrahmanyam
Date, Time / Venue : 25/8/17 2:00am -5:00pm, SCIS Seminar Room

Journal Club Seminar: STUDY OF BLOOD FLOW THROUGH A DISEASED ARTERY
Speaker: Dr. Sapna Ratan Shah, SCIS, JNU
Date, Time / Venue : 23/8/17, 3:30pm -5:00pm, Seminar Room, SCIS

Journal Club Seminar : Accurate Estimation of Protein Folding and Unfolding Times Beyond Markov State Models
Speaker : Ms. Ruhar, Research Scholar, SCIS, JNU
Date, Time / Venue : 18/8/17, 3:30pm-4:30pm, SCIS Seminar Room

Seminar : The Internet and Cyber (In)Security
Speaker : Dr. Glenn Mansfield KEENI
President & CEO, Cyber Solutions Inc. Japan.
Date, Time / Venue : 17/8/17 2:00pm -3:30pm, Seminar Room SCIS

Journal Club Seminar : Selective Ion Binding by Protein Probed with the Statistical Mechanical Integral Equation Theory
Mr. Rakesh Srivastava, Research Scholar, SCIS, JNU
Date, Time / Venue : 3/8/17 3:30pm -5:00pm, Seminar Room SCIS

SEMINAR : Interaction with Industry
" Bridging Industry-Academia Gap - Enhancing Employability & Entrepreneurship thru IBM ICE Program"

Speaker: Mr. Vithal Madyalkar
Country Manager, IBM Innovation Center for Education (ICE)
Date, Time / Venue : 20/4/17, 3:30pm - 4:30pm

Genomics and Beyond: Unveiling Gene/Genome Regulation for Translational Research in Crop Plants
Speaker:Dr. Mukesh Jain
Date, Time / Venue : 19/4/17 3:30pm - 4:30pm, Seminar Room SCIS

Pannel Discussion : Big Data Science
Heidelberg University-SC&IS, JNU joint Program
Date, Time / Venue : 11/4/17 10:00am-4:30pm, Commitee Room, SCIS

CCPM–7 Workshop
Conducted jointly by IIIT-H and JNU Delhi
(Physical and Online)

Date, Time / Venue : 10/4/17 10:00am-4:30pm , Commitee Room, SCIS

Journal Club Seminar: Mesoscopic Networks in Complex Socio-economic Systems
Speaker:Ms. Kiran Sharma
Date, Time / Venue : 6/4/17 3:30 - 4:30 pm Seminar Room No. 30, SCIS/JNU
Sponsored by DBT Govt. of India

Journal Club Seminar: How theory and computation are helpful in chemistry and biology.
Speaker: Prof. Pradipta Bandyopadhyay
Date, Time / Venue : 5/4/17 3:30pm - 4:30 pm, Seminar Room No. 30, SCIS/JNU

Seminar : Tracer dynamics in sticky mobile or frozen polymeric environment
Speaker : Dr. Rajarshi Chakrabarty (IIT Bombay)
Date, Time / Venue : 28/3/17, 3:30pm-4:30pm, Seminar Room SCIS

Seminar
Deletion of nuclear factor kappa B1 p50 subunit increases innate immune response and protects host from H. pylori colonization
Prof. Rupesh Chaturvedi (Research Director and Professor, SBT, JNU)
&
Mathematical Modeling of Biological Systems
Dr. Rakesh Pandey (DST Inspire Faculty, National Institute of Immunology, New Delhi)
Date, Time / Venue : 22/3/17, 3:30pm-5:30pm, Seminar Room SCIS

Seminar : Dried Blood Spot Based Lipid Profiling for Detection of Coronary Artery Disease using High Resolution Mass Spectroscopy.
Speaker : Dr. Narinder Singh Sahni, SCIS
Date, Time / Venue : 14/3/17 3:30pm - 5:00 pm, Seminar Room, SCIS

Journal Club Seminar : Title: Synchronization of two Hodgkin-Huxley neurons due to internal noise.
Speaker : Rahul Gupta, Research Scholar, SCIS, JNU
Date, Time / Venue : 8/2/17 3:00pm-4:00pm, Seminar Room, SCIS

Seminar : Understanding Biological Research Documents using a Neural Network Speaker : Varun Mittal
University of Washington
Date, Time / Venue : 23/1/17 3:30pm-4:30pm, Seminar Room, SCIS