Postdoctoral fellow

Michael Brenner's group, SEAS, Harvard

**Current
research interests**

Problems at the interface between materials science and
biology, approached using methods of statistical physics, soft matter and
theoretical computer science. Current research includes design of responsive nano-scale materials, design of multi-stable mechanical
objects, specificity in binding interactions, non-equilibrium
error correction and active self-assembly. Interests in high-energy physics
include gauge-gravity duality and entanglement entropy.

**Research
experience & education**** **CV

Member Institute
for Advanced Study, Princeton, NJ Aug
09 – Aug 12

Visiting Researcher Rockefeller
University, New York City, NY Aug 09 – Aug
12

PhD (Physics) Princeton
University, Princeton, NJ
Sep 04 – Jul 09

B.S. (Mathematics) California
Institute of Technology, Pasadena, CA Sep
00 – Jun 04

**Publications**

Multifarious Assembly Mixtures: Systems Allowing Retrieval
of Diverse Stored Structures, *in
collaboration with: Z. Zeravcic, S. Leibler and M. Brenner*

Under review arXiv

Principles for Robust Self-Assembly of Heterogeneous
Structures at Finite Concentration, *in
collaboration with: J. Zou, and M. Brenner*

Under review

Discriminatory proofreading regimes in non-equilibrium
systems, *in collaboration with: D.A. Huse, and S. Leibler*

Physical Review X 4 (2), 021016 PRX

Speed, dissipation, and error in kinetic proofreading, *in collaboration with: D.A. Huse,
and S. Leibler*

Proceedings of the National Academy of Sciences 109(30):12034-9 (2012) PDF SI

AdS4/CFT3 - squashed, stretched and warped, *in collaboration with: I.R.Klebanov
and T.Klose*

Journal of High Energy Physics 0903 140 (2009)
arxiv:0809.3773 [hep-th] PDF

Goldstone Bosons and Global Strings in a Warped Resolved Conifold, *in
collaboration with: I. R. Klebanov, D.
Rodriguez-Gomez and J. Ward*

Journal of High Energy Physics 0805, 090 (2008),
arXiv:0712.2224 [hep-th] PDF

Entanglement as a Probe of Confinement, *in collaboration with: I. R. Klebanov
and D. Kutasov*

Nuclear Physics B 796, 274 (2008), arXiv:0709.2140 [hep-th] PDF

Gauge/Gravity Duality and Warped Resolved Conifold, *in collaboration with: I. R. Klebanov*

Journal of High Energy Physics 0703, 042 (2007), arXiv:hep-th/0701064 PDF

On D3-brane potentials in compactifications
with fluxes and wrapped D-branes

*in** collaboration with: D. Baumann,
A. Dymarsky, I. R. Klebanov,
J. M. Maldacena and L. P. McAllister*

Journal of High Energy Physics 0611, 031 (2006), arXiv:hep-th/0607050 PDF

Fatgraph
expansion for noncritical superstrings, *in
collaboration with: A. Kapustin*

arXiv:hep-th/0404238 (2004)
PDF

**Links**

SEAS
Calendar Arxiv Web of Knowledge

**Design principles for heterogeneous self-assembly**

Self-assembly is a bottom-up method of assembling
structures from interacting particles. Local control parameters — like binding
energies between different species of particles and their concentrations — are
chosen to pick out a spontaneous assembly of a desired structure. However, in
real systems, many undesired structures are also produced. We show that
self-assembly is enhanced by choosing control parameters that are 'off-target' ; for example, the optimal supply of components to
produce a structure A-B-A might be supplying A and B in a ratio of 100 to 1
(instead of 2 to 1), depending on the physics of assembly and the undesirablity of various competing structures formed. Such
'off-target' rules strike a balance between
enhancing the desired stricture and suppressing undesired ones.

In general, the control parameters cannot be chosen
based on the desired structure alone and need to reflect a balance between
desired and undesired structures.

**Principles
for Robust Self-Assembly of Heterogeneous Structures at Finite Concentration**, (submitted) *with
James Zou and Michael Brenner.*

**Towards an information theory of 'shape': specificity in natural and
synthetic systems**

A wide range of natural and
synthetic systems rely on the existence of specific interactions between
several species of particles (or binding sites). The physics and
chemistry of interaction between particles limit the number of unique 'lock and
key’ pairs that a system can support without significant `cross-talk’ (i.e.,
undesired interactions) across pairs. Such a limit is at the heart of many
phenomena, from functioning of the immune system, signaling pathways,
artificial molecular sensors ('artificial noses') and synthetic self-assembly.
Inspired by on Shanon's theory of coding, we develop
a framework on coding specific interactions using shape and surface chemistry.
Our framework reveals how different aspects of physical interactions affect the
amount of information that can be encoded in particle interactions.

**An
information theory of 'shape', **(in preparation) *with Miriam
Huntley and Michael Brenner.*

**Non-equilibrium error correction**

It is widely appreciated that energy is required to
carry out mechanical work. At the molecular scale in biology, energy is used to
maintain order and correct 'errors' in various biochemical processes. For
example, the error rate in DNA replication and protein synthesis is much lower
than expectations from equilibrium thermodynamics. The low
error rate in such enzymatic reactions has been explained using the
non-equilibrium mechanism of `Kinetic Proofreading' by John Hopfield and
Jacques Ninio. What are the general principles
behind this mechanism? How would you program a general non-equilibrium system
with such 'error correcting' ability? Can you incorporate these ideas into
materials synthesis methods, using energy to fix errors in synthesis?

We show that the central principle behind kinetic
proofreading is ``dynamic instability'' along the reaction coordinate. That is,
a reaction, while proceeding from start to finish, must be repeatedly reset to
earlier stages using energy from an external source. This coarse-grained view
of kinetic proofreading connects the original enzymatic mechanism to diverse
phenomena, such as microtubule growth and foraging and search strategies. Our
view also reveals fundamental trade-offs between speed, energy and accuracy,
including a regime with a large gain in speed at a small cost in accuracy.
We are working to implement these principles in synthetic systems (for e.g, hybridization of DNA strands), using DNA strand
displacement as an energy source.

**Speed, dissipation, and error in
kinetic proofreading, ***with: D.A. Huse, and S. Leibler* PNAS
109(30):12034-9 (2012) SI

**Discriminatory proofreading
regimes in non-equilibrium systems, ***with: D.A. Huse, and S. Leibler *Phys. Rev.
X 4, 021016 (2014)

Quantum entanglement has been a
fruitful idea in many areas of physics but until recently, it had not found
much use in particle physics. We proposed entanglement between quarks as a
subtle test of whether quarks are inseparably bound (``confined'') in any given
theory of quarks and gluons. Our proposal was validated by
lattice simulations by groups at Argonne National Labs/U Chicago and ITEP
(Moscow). Entanglement entropy has since found many other applications in
particle physics and string theory and has become a popular area of research in
recent years.

**Entanglement as a
probe of Confinement**, *with David Kutasov
and Igor Klebanov**,*
Nuclear Physics B
(796), 274 (2008)

**Geometric interpretations of
problems in inflationary cosmology and renormalization group theory**

The AdS/CFT
correspondence shows how problems in particle physics can be mathematically
translated to geometric problems in Einstein’s theory of gravity in higher
dimensional spacetimes. We used this correspondence
to show how difficult calculations in models of inflationary cosmology could be
solved easily using the geometric interpretation. For example, it is
difficult to derive predictions from some models of inflationary cosmology due
to strongly interacting quantum fields present in such models. We showed that
this problem was equivalent to a simpler system of gravitational interactions a
particle and a membrane in curved spacetimes.

I also studied other strongly interacting behavior
in quantum field theories (renormalization group flows, conformal field theory)
using geometric problems in gravity through the AdS/CFT
correspondence.

**On D3-brane potentials in compactifications with fluxes and wrapped D-branes,
with**

**Gauge/Gravity Duality and Warped
Resolved Conifold, ***with:
I. R. Klebanov* PDF

**AdS4/CFT3 - squashed, stretched and
warped, with**

**Goldstone Bosons and Global Strings in
a Warped Resolved Conifold, ***with: I. R. Klebanov, D.
Rodriguez-Gomez and J. Ward* PDF

**Fatgraph**** expansion for noncritical superstrings,**** ***with: A. Kapustin *PDF