Hamiltonian simulation with optimal sample complexity

© 2017 Author(s). We investigate the sample complexity of Hamiltonian simulation: how many copies of an unknown quantum state are required to simulate a Hamiltonian encoded by the density matrix of that state? We show that the procedure proposed by Lloyd, Mohseni, and Rebentrost [Nat. Phys., 10(9):631-633, 2014] is optimal for this task. We further extend their method to the case of multiple input states, showing how to simulate any Hermitian polynomial of the states provided. As applications, we derive optimal algorithms for commutator simulation and orthogonality testing, and we give a protocol for creating a coherent superposition of pure states, when given sample access to those states. We also show that this sample-based Hamiltonian simulation can be used as the basis of a universal model of quantum computation that requires only partial swap operations and simple single-qubit states.S.K. and C.Y.L. are funded by the Department of Defense. G.H.L. is funded by the NSF CCR and the ARO quantum computing projects. M.O. acknowledges Leverhulme Trust Early Career Fellowship (ECF-2015-256) and European Union project QALGO (Grant Agreement No. 600700) for financial support. T.J.Y. thanks the DoD, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a. The authors are grateful to the University of Maryland Libraries’ Open Access Publishing Fund and the Massachusetts Institute of Technology Open Access Publishing Fund for partial funding for open access

Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA – microRNA regulatory network in nasopharyngeal carcinoma model systems

Nasopharyngeal carcinoma (NPC) is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq) of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein-Barr virus (EBV)-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV) to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA-mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL), single nucleotide variant (SNV), and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies. © 2014 The Authors.published_or_final_versio

Quantum Algorithms for the Most Frequently String Search, Intersection of Two String Sequences and Sorting of Strings Problems

We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the string that occurs in the sequence most often. We propose a quantum algorithm that has a query complexity $\tilde{O}(n \sqrt{k})$. This algorithm shows speed-up comparing with the deterministic algorithm that requires $\Omega(nk)$ queries. The second one is searching intersection of two sequences of strings. All strings have the same length $k$. The size of the first set is $n$ and the size of the second set is $m$. We propose a quantum algorithm that has a query complexity $\tilde{O}((n+m) \sqrt{k})$. This algorithm shows speed-up comparing with the deterministic algorithm that requires $\Omega((n+m)k)$ queries. The third problem is sorting of $n$ strings of length $k$. On the one hand, it is known that quantum algorithms cannot sort objects asymptotically faster than classical ones. On the other hand, we focus on sorting strings that are not arbitrary objects. We propose a quantum algorithm that has a query complexity $O(n (\log n)^2 \sqrt{k})$. This algorithm shows speed-up comparing with the deterministic algorithm (radix sort) that requires $\Omega((n+d)k)$ queries, where $d$ is a size of the alphabet.Comment: THe paper was presented on TPNC 201

A computational model of liver iron metabolism

Iron is essential for all known life due to its redox properties; however, these same properties can also lead to its toxicity in overload through the production of reactive oxygen species. Robust systemic and cellular control are required to maintain safe levels of iron, and the liver seems to be where this regulation is mainly located. Iron misregulation is implicated in many diseases, and as our understanding of iron metabolism improves, the list of iron-related disorders grows. Recent developments have resulted in greater knowledge of the fate of iron in the body and have led to a detailed map of its metabolism; however, a quantitative understanding at the systems level of how its components interact to produce tight regulation remains elusive. A mechanistic computational model of human liver iron metabolism, which includes the core regulatory components, is presented here. It was constructed based on known mechanisms of regulation and on their kinetic properties, obtained from several publications. The model was then quantitatively validated by comparing its results with previously published physiological data, and it is able to reproduce multiple experimental findings. A time course simulation following an oral dose of iron was compared to a clinical time course study and the simulation was found to recreate the dynamics and time scale of the systems response to iron challenge. A disease state simulation of haemochromatosis was created by altering a single reaction parameter that mimics a human haemochromatosis gene (HFE) mutation. The simulation provides a quantitative understanding of the liver iron overload that arises in this disease. This model supports and supplements understanding of the role of the liver as an iron sensor and provides a framework for further modelling, including simulations to identify valuable drug targets and design of experiments to improve further our knowledge of this system

Hamiltonian simulation with optimal sample complexity

© 2017 Author(s). We investigate the sample complexity of Hamiltonian simulation: how many copies of an unknown quantum state are required to simulate a Hamiltonian encoded by the density matrix of that state? We show that the procedure proposed by Lloyd, Mohseni, and Rebentrost [Nat. Phys., 10(9):631-633, 2014] is optimal for this task. We further extend their method to the case of multiple input states, showing how to simulate any Hermitian polynomial of the states provided. As applications, we derive optimal algorithms for commutator simulation and orthogonality testing, and we give a protocol for creating a coherent superposition of pure states, when given sample access to those states. We also show that this sample-based Hamiltonian simulation can be used as the basis of a universal model of quantum computation that requires only partial swap operations and simple single-qubit states