Evolution of Protein Molecules

THE JOURNAL OF BIOLOGICAL CHEMISTRY: The Biochemical Behavior of LeadL I. Influence of Calcium, Phosphorus, and Vitamin D on Lead in Blood and Bone

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.

http://science.sciencemag.org/content/sci/332/6034/1196.full.pdf

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.

/pdf/peaks-powerful-software-for-peptide-de-novo-sequencing-by-1htzy7q8mi.pdf

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

The impressive capabilities of the mammalian brain—ranging from perception, pattern recognition and memory formation to decision making and motor activity control—have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the ‘intelligent’ behaviour required for survival However, the study of how molecules can ‘think’ has not produced an equal variety of computational models and applications of artificial chemical systems Although biomolecular systems have been hypothesized to carry out neural-network-like computations in vivo and the synthesis of artificial chemical analogues has been proposed theoretically, experimental work has so far fallen short of fully implementing even a single neuron Here, building on the richness of DNA computing and strand displacement circuitry, we show how molecular systems can exhibit autonomous brain-like behaviours Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, we systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks Our approach even allows us to implement a Hopfield associative memory with four fully connected artificial neurons that, after training in silico, remembers four single-stranded DNA patterns and recalls the most similar one when presented with an incomplete pattern Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment

/pdf/neural-network-computation-with-dna-strand-displacement-2m7egtgffn.pdf

Neural network computation with DNA strand displacement cascades

This paper studies how to concurrently permute related logical or physical submeshes in a d-dimensional n/spl times/.../spl times/n physical mesh via wormhole and dimension-ordered routing. Our objective is to minimize the congestion for realizing the permutations, while maximizing the number and dimensionality of permuted submeshes. We show that for d/spl les/2/spl alpha/+/spl beta/, concurrent independent permutations of n/sup /spl beta// related physical submeshes, each of /spl alpha/ dimensions, can be performed in two routing steps without congestion. If the permuted submeshes are logical ones, they can be permuted in one, instead of two, routing step. In addition, any shift operation along any axis of the logical mesh can be performed in the physical mesh without congestion. We also show that if all nodes know the permutation function, any permutation within a submesh of dimensions [2(d-1)/3] can be realized in three routing steps without congestion. >

Efficient submesh permutations in wormhole-routed meshes

In this paper, we study the problem of designing proxies (or portfolios) for various stock market indices based on historical data. We use four different methods for computing market indices, all of which are formulae used in actual stock market analysis. For each index, we consider three criteria for designing the proxy: the proxy must either track the market index, outperform the market index, or perform within a margin of error of the index while maintaining a low volatility. In eleven of the twelve cases (all combinations of four indices with three criteria except the problem of sacrificing return for less volatility using the price-relative index) we show that the problem is NP-hard, and hence most likely intractable.

/pdf/designing-proxies-for-stock-market-indices-is-sbdw0adaqv.pdf

Designing proxies for stock market indices is computationally hard

Given a multiset $X=\{x_1,..., x_n\}$ of real numbers, the {\it floating-point set summation} problem asks for $S_n=x_1+...+x_n$. Let $E^*_n$ denote the minimum worst-case error over all possible orderings of evaluating $S_n$. We prove that if $X$ has both positive and negative numbers, it is NP-hard to compute $S_n$ with the worst-case error equal to $E^*_n$. We then give the first known polynomial-time approximation algorithm that has a provably small error for arbitrary $X$. Our algorithm incurs a worst-case error at most $2(\mix)E^*_n$.\footnote{All logarithms $\log$ in this paper are base 2.} After $X$ is sorted, it runs in O(n) time. For the case where $X$ is either all positive or all negative, we give another approximation algorithm with a worst-case error at most $\lceil\log\log n\rceil E^*_n$. Even for unsorted $X$, this algorithm runs in O(n) time. Previously, the best linear-time approximation algorithm had a worst-case error at most $\lceil\log n\rceil E^*_n$, while $E^*_n$ was known to be attainable in $O(n \log n)$ time using Huffman coding.

Linear-Time Approximation Algorithms for Computing Numerical Summation with Provably Small Errors

This paper studies some basic problems in a multiple-object auction model using methodologies from theoretical computer science. We are especially concerned with situations where an adversary bidder knows the bidding algorithms of all the other bidders. In the two-bidder case, we derive an optimal randomized bidding algorithm, by which the disadvantaged bidder can procure at least half of the auction objects despite the adversary's a priori knowledge of his algorithm. In the general $k$-bidder case, if the number of objects is a multiple of $k$, an optimal randomized bidding algorithm is found. If the $k-1$ disadvantaged bidders employ that same algorithm, each of them can obtain at least $1/k$ of the objects regardless of the bidding algorithm the adversary uses. These two algorithms are based on closed-form solutions to certain multivariate probability distributions. In situations where a closed-form solution cannot be obtained, we study a restricted class of bidding algorithms as an approximation to desired optimal algorithms.

Optimal Bidding Algorithms Against Cheating in Multiple-Object Auctions

Mee Yee Chan a, Wun-Tat Chanb, Francis Y.L. China, Stanley P.Y. Fungc and Ming-Yang Kaod aDepartment of Computer Science, University of Hong Kong, Hong Kong, China bCollege of International Education, Hong Kong Baptist University, Hong Kong, China cDepartment of Computer Science, University of Leicester, Leicester, UK dDepartment of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL, USA

Ming-Yang Kao

Papers

Efficient submesh permutations in wormhole-routed meshes

Designing proxies for stock market indices is computationally hard

Linear-Time Approximation Algorithms for Computing Numerical Summation with Provably Small Errors

Optimal Bidding Algorithms Against Cheating in Multiple-Object Auctions

Haplotype inference on pedigrees without recombinations