TY - THES
AB - A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.
Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing.
AU - Mckenzie, Catherine
ID - 7132
SN - 2663-337X
TI - Design and characterization of methods and biological components to realize synthetic neurotransmission
ER -
TY - JOUR
AB - Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.
AU - Kühnen, Jakob
AU - Scarselli, Davide
AU - Hof, Björn
ID - 6486
IS - 11
JF - Journal of Fluids Engineering
SN - 00982202
TI - Relaminarization of pipe flow by means of 3D-printed shaped honeycombs
VL - 141
ER -
TY - JOUR
AB - Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.
AU - Scarselli, Davide
AU - Kühnen, Jakob
AU - Hof, Björn
ID - 6228
JF - Journal of Fluid Mechanics
SN - 00221120
TI - Relaminarising pipe flow by wall movement
VL - 867
ER -
TY - CONF
AB - In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Pourdamghani, Arash
ID - 6378
SN - 9781450359337
T2 - Proceedings of the 34th ACM Symposium on Applied Computing
TI - Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving
VL - Part F147772
ER -
TY - CONF
AB - In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a
given probabilistic program terminates with probability 1. Scalable approaches for program analysis often
rely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)
of Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure
termination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the
proposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed
modular rule is still not sound for almost-sure termination of probabilistic programs.
Besides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a
sound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel
notion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales
that are linear and show that they can be synthesized in polynomial time. Finally, we present experimental
results on a variety of benchmarks and several natural examples that model various types of nested while
loops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure
termination property
AU - Huang, Mingzhang
AU - Fu, Hongfei
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
ID - 6780
T2 - Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications
TI - Modular verification for almost-sure termination of probabilistic programs
VL - 3
ER -
TY - CONF
AB - We consider the problem of expected cost analysis over nondeterministic probabilistic programs,
which aims at automated methods for analyzing the resource-usage of such programs.
Previous approaches for this problem could only handle nonnegative bounded costs.
However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,
both positive and negative costs are necessary and the costs are unbounded as well.
In this work, we present a sound and efficient approach to obtain polynomial bounds on the
expected accumulated cost of nondeterministic probabilistic programs.
Our approach can handle (a) general positive and negative costs with bounded updates in
variables; and (b) nonnegative costs with general updates to variables.
We show that several natural examples which could not be
handled by previous approaches are captured in our framework.
Moreover, our approach leads to an efficient polynomial-time algorithm, while no
previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime.
Finally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds.
AU - Wang, Peixin
AU - Fu, Hongfei
AU - Goharshady, Amir Kafshdar
AU - Chatterjee, Krishnendu
AU - Qin, Xudong
AU - Shi, Wenjun
ID - 6175
KW - Program Cost Analysis
KW - Program Termination
KW - Probabilistic Programs
KW - Martingales
T2 - PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation
TI - Cost analysis of nondeterministic probabilistic programs
ER -
TY - CONF
AB - Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.
Two classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.
In this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Goharshady, Ehsan Kafshdar
ID - 6490
SN - 9781450359337
T2 - Proceedings of the 34th ACM Symposium on Applied Computing
TI - The treewidth of smart contracts
VL - Part F147772
ER -
TY - JOUR
AB -
Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.
Our main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Goyal, Prateesh
AU - Ibsen-Jensen, Rasmus
AU - Pavlogiannis, Andreas
ID - 7158
IS - 4
JF - ACM Transactions on Programming Languages and Systems
SN - 0164-0925
TI - Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth
VL - 41
ER -
TY - CONF
AB - In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Pourdamghani, Arash
ID - 6056
T2 - IEEE International Conference on Blockchain and Cryptocurrency
TI - Probabilistic smart contracts: Secure randomness on the blockchain
ER -
TY - JOUR
AB - We study the problem of developing efficient approaches for proving
worst-case bounds of non-deterministic recursive programs. Ranking functions
are sound and complete for proving termination and worst-case bounds of
nonrecursive programs. First, we apply ranking functions to recursion,
resulting in measure functions. We show that measure functions provide a sound
and complete approach to prove worst-case bounds of non-deterministic recursive
programs. Our second contribution is the synthesis of measure functions in
nonpolynomial forms. We show that non-polynomial measure functions with
logarithm and exponentiation can be synthesized through abstraction of
logarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem
using linear programming. While previous methods obtain worst-case polynomial
bounds, our approach can synthesize bounds of the form $\mathcal{O}(n\log n)$
as well as $\mathcal{O}(n^r)$ where $r$ is not an integer. We present
experimental results to demonstrate that our approach can obtain efficiently
worst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the
divide-and-conquer algorithm for the Closest-Pair problem, where we obtain
$\mathcal{O}(n \log n)$ worst-case bound, and (ii) Karatsuba's algorithm for
polynomial multiplication and Strassen's algorithm for matrix multiplication,
where we obtain $\mathcal{O}(n^r)$ bound such that $r$ is not an integer and
close to the best-known bounds for the respective algorithms.
AU - Chatterjee, Krishnendu
AU - Fu, Hongfei
AU - Goharshady, Amir Kafshdar
ID - 7014
IS - 4
JF - ACM Transactions on Programming Languages and Systems
TI - Non-polynomial worst-case analysis of recursive programs
VL - 41
ER -