Rama Ratnam


Senior Scientist

University of Illinois at Urbana-Champaign


Coordinated Science Laboratory,

University of Illinois at Urbana-Champaign,

1308 West Main Street,

Urbana, IL 61801, USA.



1208 Health Care Engineering Systems Center,

1206 CSL Studio, W. Clark St., Urbana, IL 61801.

(217) 300-6203

Email: ratnam [at] illinois [dot] edu



Animal neurophysiology: 2524 Beckman Institute.

Human neurophysiology: B18 Coordinated Science Laboratory. 




Coordinated Science Laboratory

Beckman Institute for Advanced Science and Technology

The Neuroscience Program


Education and training


B. Tech., Chemical Engineering, Indian Institute of Technology, Delhi, 1985.

Ph.D., Biophysics, University of Illinois at Urbana-Champaign, Urbana, 1998.

Post-doctoral research associate, Department of Molecular & Integrative Physiology, and the Beckman Institute, University of Illinois at Urbana-Champaign, 1998-2001.

Research Scientist, The Intelligent Hearing Aid Project, Beckman Institute, University of Illinois at Urbana-Champaign, 2001-2004.




Some details on my academic background, work experience, and a brief digression into my academic lineage can be found in this link [Biosketch].


Research interests


Neurophysiology, biophysics, theoretical and computational neuroscience, sensory physiology, animal behavior, and neural engineering.


More specifically, 1) determining the coding of a sensory stimulus by single-neurons using in vivo electrophysiology, theory, and computations, 2) determining biophysical mechanisms and models of single-neuron coding, and 3) the use of optimal neural codes for speech vocoding in cochlear implants.


The model systems I work with are the auditory system of the gerbil and the electrosensory system of weakly electric fish.


I have an active interest in vocal communication behavior, particularly in songbirds, and in anurans (frogs and toads) where I study male-male vocal interactions in dense choruses using a microphone array. In recent years I have developed an interest in human body motion capture using depth-sensing cameras for calculating inverse dynamics. I hope that this will lead to understanding neuromuscular and sensorimotor control, and proprioceptive feedback in posture and movement.


For more details, see "Interests" below.


Research projects


1.       Optimal sound coding in the auditory nerve of the anesthetized gerbil.

2.       Biophysical, conductance-based models of stimulus coding in single-neurons, constrained by experimental data.

3.       Theoretical development of optimal neural coding as source coding.

4.       Speech vocoding for cochlear implants using a timing-based optimal neural code.

5.       Determining human body dynamics from motion capture data, with the aim of assessing fall-risk in the elderly.

6.       Song variation in the golden-cheeked warbler (Setophaga chrysoparia).


Doctoral students




1.       Alexander R. Asilador (in progress, Neuroscience program, University of Illinois).




1.       Erik C Johnson (2016, Electrical and Computer Engineering, University of Illinois; co-supervised with Douglas L. Jones)

2.       Michelle D. Valero (2012, Neuroscience program, Department of Biology, University of Texas at San Antonio)




I do not teach at Illinois other than offering sundry guest lectures. I did teach when I was on the faculty in the biology department at the University of Texas at San Antonio.


List of classes where I was the instructor, provided guest lectures, and was a teaching assistant.




List of things I have done for my institutions.




List of it.




I have many wonderful collaborators. They are students, postdocs, engineers, field biologists, and faculty. I cannot mention them all. However, my major collaborator since 2001 (and counting) is Douglas L. Jones (Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign). Doug and I have worked on a range of problems at the interface between biology, engineering, and acoustics. These include, the blind estimation of acoustic reverberation time, the use of microphone arrays for monitoring frog choruses, and development of remote wildlife acoustic monitoring systems. Our ongoing work (since 2010) is on optimal neural coding, and the development of speech vocoders for cochlear implants using principles of optimal neural coding.




Someone once said that "it is not a problem when your hobbies interfere with your work. It is only a problem when your hobbies interfere with one another." My life has been a very serious struggle between academic and non-academic interests, sometimes tilting here and sometimes tilting there. However, I will write only about academic interests.


1.   As I get older and mature as a biologist I find myself leaning more and more towards evolutionary biology, particularly the adaption of biophysical mechanisms due to selective pressure. Of these mechanisms, the neural code, its origins, its biophysical substrate, and its subsequent shaping of animal behavior, is a deep problem worthy of investigation. The central question here is how good is the representation of the external world in the sensory periphery? Has selective pressure resulted in the best possible representation of the sensory world? If so, how do we show this at both physiological time-scales and evolutionary time scales? I have been working on the neural code at a physiological level for some years, and I hope to pursue the larger question, that of ultimate causation, when I get more time.


2.   There are some model systems that I go back to over and over again. They are, in some sense, my first love. In them I can see the eternal struggle between change and adaptation. They reveal with great clarity the structure of evolutionary processes.


a)   The first system is the vocal communication system in anurans (frogs and toads). Male vocal communication behavior and female mate choice are among the most beautiful examples of the links between proximate and ultimate mechanisms in sexual selection. The males have one function, and one alone: to show up every evening during the breeding season, attract females, and donate sperm. Female mate choice exerts demanding selective pressure, and males have responded by shaping the dynamics of calling to increase the chances of attracting females. In 1989 Peter Narins (at UCLA) was the first to suggest that the male calling system in the Puerto Rican Coqui frog is similar to digital communications. A single call acts  as a discrete "packet". Recently, and more than twenty years later, Doug Jones and I used microphone array processing to sharpen and extend Narin's findings in the American green treefrog. We showed that these frogs perform a kind of optimized digital communication using discrete phase hopping to (presumably) avoid acoustic interference. It is remarkable that a system of loosely coupled physiological oscillators has converged on to features found in digital comm. There is so much more to explore here.


b)   The second system is the structure of bird song and how it can change (I am not talking about songbird learning, but rather of sudden or abrupt changes in some direction in song syllables).  The endangered golden-cheeked warbler (Setophaga chrysoparia), found largely in the Edwards's plateau in central Texas, has modified one syllable in its so-called Type B song. The shift is from a buzzy trill to an exquisite downward and upward frequency modulation that introduces a rather sweet lilt to the voice. Why has it done this, particularly when its Type A song is intact? In a field study spanning several years (by my collaborator Wendy Leonard, a Park Ranger with San Antonio Parks and Recreation) we showed that there is a definite modification of a particular song syllable from songs recorded in the early to mid-1990s and those recorded ten years later, and these modifications also occur over a wide transect of over a 150 kms. We have however, only scratched the surface and there are deep questions here, particularly concerning the malleability of one voice (Type B song) over the other (Type A song). The frog and warbler bioacoustics projects require me to be out in the field and collect data. Texas is great for that.


c)   The third system is the active electrosensory system of weakly electric fish. The neurons producing the oscillating electric organ discharge in the fish are among the most precisely timed biological pacemakers. In engineering terms the electric organ discharge is a High-Q, extremely narrow-band oscillator that provides a private channel for executing short-range sensing and navigation. I believe (as does my colleague Doug Jones) that this tuned narrow-band signal is the ideal, albeit highly specialized system to investigate optimal neural coding of sensory signals.


In neuroethology, and behavioral neuroscience in general, specialized sensory systems are interesting because they reveal biological mechanisms not necessarily obvious in less specialized systems (such as passive mammalian hearing). The sound localization circuits in the barn owl (Mark Konishi's work) as also echolocation in bats are two such specialized systems, as also jamming avoidance in wave-type electric fish (Walter Heiligenberg's work). The electric fish continues to provide wonderful insights into sensory processing, even though the electric sense is irrelevant to mammals (including the most egotistic mammal of all).


3.   Another problem that goes back to my early years when I abandoned control theory for neuroscience is the problem of a central neural controller that regulates muscle tone to maintain posture and balance, and then actively guides movement when needed. If you consider the number of degrees of freedom available to the major joints (some 20 joints, at a minimum) and their coupling, including imposition of constraints and contact forces, the resultant Jacobian and Coriolis matrices become massive. The only direct feedback are through the vestibular system and the proprioceptive receptors found in muscle, tendons, and ligaments, and indirect feedback through visual and somatosensory systems. How is a controller structure even realized in this high-dimensional, highly nonlinear system? Which states are observable and controllable? Further, how does the controller adapt (or decline) as we grow older or suffer insults and traumas? This is a rich problem at the intersection of neuroscience, integrative physiology, kinematics, forward and inverse dynamics, and control theory. Surely, we can make a go of it, no?


4.   Is it possible to remove the cochlea, replace it with a processor and a micro-electrode array implant that drives the auditory nerve, so that the nervous system can't tell the difference? A sort of bionic ear. Cochlear implants should do this but they do not recreate the same pattern of electrical activity as the intact cochlea. This is a nice plug-and-play problem, but I suspect really hard because of problems with figuring out the correct neural code, getting the anatomy right for surgical implantation, developing bio-compatible materials, etc. Moving towards this kind of neural implant is a worthy goal.



There is so much to write about.... [Other Writings].


... and so many books to read. [Readings].

External links, and why there are none of them


In the early 1990s, when I first started graduate work in biophysics at the University of Illinois, I was with the late Professor Klaus Schulten's group (Theoretical Biophysics). We were on the 3rd floor of the Beckman Institute. The National Center for Supercomputing Applications (NCSA) was located up on the 5th floor of the Beckman and we were heavy users of the supercomputers at NCSA, not to mention doing summer jobs for them. So it was obvious that we would use Mosaic, the first web browser ever, originally developed at NCSA. It was a new toy and we wondered what we could do with it. One thing we discovered rather quickly: we could link to other pages (there were no "web" sites then, just pages). Now, this was just so cool.


So, our pages also included links to other pages around the world. There weren't too many of them so it wasn't too hard. Some among us were so desperate to create content that in certain pathological and degenerate cases, there were pages that only provided links to other pages. In later years it prompted us to add a small line at the bottom of our web page saying "Wasn't it great when every web page had a link to every other web page in the world?"


It would take too much space here to provide you with a link to every web page in the world. So, it is better to not provide any links at all.


"It's not my fault. It was the algorithm!"

Modified by Ratnam, Tuesday, October 11, 2017, 9:47 PM, Urbana, Illinois, USA.

Created by Ratnam, Tuesday, July 18, 2017, Urbana, Illinois, USA.