arXiv subjects

Junhua Zhang

Publications and source records attributed to Junhua Zhang.

At least 37 records · Page 2Linked to original sources

arXiv2016

Discovery of cancer common and specific driver gene sets

Cancer is known as a disease mainly caused by gene alterations. Discovery of mutated driver pathways or gene sets is becoming an important step to understand molecular mechanisms of carcinogenesis. However, systematically investigating commonalities and specificities of driver gene sets among multiple cancer types is still a great challenge, but this investigation will undoubtedly benefit deciphering cancers and will be helpful for personalized therapy and precision medicine in cancer treatment. In this study, we propose two optimization models to \emph{de novo} discover common driver gene sets among multiple cancer types (ComMDP) and specific driver gene sets of one certain or multiple cancer types to other cancers (SpeMDP), respectively. We first apply ComMDP and SpeMDP to simulated data to validate their efficiency. Then, we further apply these methods to 12 cancer types from The Cancer Genome Atlas (TCGA) and obtain several biologically meaningful driver pathways. As examples, we construct a common cancer pathway model for BRCA and OV, infer a complex driver pathway model for BRCA carcinogenesis based on common driver gene sets of BRCA with eight cancer types, and investigate specific driver pathways of the liquid cancer lymphoblastic acute myeloid leukemia (LAML) versus other solid cancer types. In these processes more candidate cancer genes are also found.

q-bio.GN↗

arXiv2016

Experimental Preparation of High NOON States for Phonons

Multi-party entangled states have important applications in quantum metrology and quantum computation. Experimental preparation of large entangled state, in particular, the NOON states, however, remains challenging as the particle number $N$ increases. Here we develop a deterministic method to generate arbitrarily high NOON states for phonons and experimentally create the states up to $N=9$ phonons in two radial modes of a single trapped \Yb ion. We demonstrate that the fidelity of the NOON states are significantly above the classical limit by measuring the interference contrast and the population through the projective phonon measurement of two motional modes. We also measure the quantum Fisher information of the generated NOON state and observe the Heisenberg scaling in the lower bounds of the phase sensitivity as the $N$ increases. Our scheme is generic and applicable to other photonic or phononic systems.

quant-ph↗

arXiv2016

Vacuum Measurements and Quantum State Reconstruction of Phonons

A quantum state is fully characterized by its density matrix or equivalently by its quasiprobabilities in phase space. A scheme to identify the quasiprobabilities of a quantum state is an important tool in the recent development of quantum technologies. Based on our highly efficient vacuum measurement scheme, we measure the quasiprobability $Q$-function of the vibrational motion for a \Yb ion {\it resonantly} interacting with its internal energy states. This interaction model is known as the Jaynes-Cummings model which is one of the fundamental models in quantum electrodynamics. We apply the capability of the vacuum measurement to study the Jaynes-Cummings dynamics, where the Gaussian peak of the initial coherent state is known to bifurcate and rotate around the origin of phase space. They merge at the so-called revival time at the other side of phase space. The measured $Q$-function agrees with the theoretical prediction. Moreover, we reconstruct the Wigner function by deconvoluting the $Q$-function and observe the quantum interference in the Wigner function at half of the revival time, where the vibrational state becomes nearly disentangled from the internal energy states and forms a superposition of two composite states. The scheme can be applied to other physical setups including cavity or circuit-QED and optomechanical systems.

quant-ph↗

arXiv2016

Topological Yu-Shiba-Rusinov chain in monolayer transition-metal dichalcogenide superconductors

Monolayers of transition-metal dichalcogenides (TMDs) are two-dimensional materials whose low energy sector consists of two inequivalent valleys. The valence bands have a large spin splitting due to strong spin-orbit coupling. Furthermore the spin is polarized up in one valley and down in the other (in directions perpendicular to the two-dimensional crystal). We focus on lightly hole-doped systems where the Fermi surface consists of two disconnected circles with opposite spins. For both proximity induced and intrinsic local attractive interaction induced superconductivity, a fully gapped intervalley pairing state is favored in this system, which is an equal superposition of the singlet and the m=0 triplet for the lack of centrosymmetry. We show that a ferromagnetically ordered magnetic-adatom chain placed on a monolayer TMD superconductor provides a platform to realize one-dimensional topological superconducting state characterized by the presence of Majorana zero modes at its ends. We obtain the topological phase diagram and show that the topological superconducting phase is affected not only by the adatom spacing and the direction of the magnetic moment, but also by the orientation of the chain relative to the crystal.

cond-mat.supr-con↗

arXiv2016

The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms

The pathogenesis of cancer in human is still poorly understood. With the rapid development of high-throughput sequencing technologies, huge volumes of cancer genomics data have been generated. Deciphering those data poses great opportunities and challenges to computational biologists. One of such key challenges is to distinguish driver mutations, genes as well as pathways from passenger ones. Mutual exclusivity of gene mutations (each patient has no more than one mutation in the gene set) has been observed in various cancer types and thus has been used as an important property of a driver gene set or pathway. In this article, we aim to review the recent development of computational models and algorithms for discovering driver pathways or modules in cancer with the focus on mutual exclusivity-based ones.

q-bio.GN↗

arXiv2015

Topological superconductivity in a multichannel Yu-Shiba-Rusinov chain

Chains of magnetic atoms placed on the surface of an s-wave superconductor with large spin-orbit coupling provide a promising platform for the realization of topological superconducting states characterized by the presence of Majorana zero-energy modes. In this work we study the properties of the one-dimensional chain of Yu-Shiba-Rusinov states induced by magnetic impurities using a realistic model for the magnetic atoms that include the presence of multiple scattering channels. These channels are mixed by the spin-orbit coupling and, via the hybridization of the Yu-Shiba-Rusinov states at different sites of the chain, result in a multi-band structure for the chain. We obtain the topological phase diagram for such band structure. We identify the parameter regimes for which the different bands lead to a topological phase and show that the inclusion of higher bands can greatly enlarge the phase space for the realization of topological states.

cond-mat.supr-con↗

arXiv2015

Realization of near-deterministic arithmetic operations and quantum state engineering

Quantum theory is based on a mathematical structure totally different from conventional arithmetic. Due to the symmetric nature of bosonic particles, annihilation or creation of single particles translates a quantum state depending on how many bosons are already in the given quantum system. This proportionality results in a variety of non-classical features of quantum mechanics including the bosonic commutation relation. The annihilation and creation operations have recently been implemented in photonic systems. However, this feature of quantum mechanics does not preclude the possibility of realizing conventional arithmetic in quantum systems. We implement conventional addition and subtraction of single phonons for a trapped \Yb ion in a harmonic potential. In order to realize such operations, we apply the transitionless adiabatic passage scheme on the anti-Jaynes-Cummings coupling between the internal energy states and external motion states of the ion. By performing the operations on superpositions of Fock states, we realize the hybrid computation of classical arithmetic in quantum parallelism, and show that our operations are useful to engineer quantum states. Our single-phonon operations are nearly deterministic and robust against parameter changes, enabling handy repetition of the operations independently from the initial state of the atomic motion. We demonstrate the transform of a classical state to a nonclassical one of highly sub-Poissonian phonon statistics and a Gaussian state to a non-Gaussian state, by applying a sequence of the operations. The operations implemented here are the Susskind-Glogower phase operators, whose non-commutativity is also demonstrated.

quant-ph↗

arXiv2015

Testing nonclassicality and non-Gaussianity in phase space

We theoretically propose and experimentally demonstrate a nonclassicality test of single-mode field in phase space, which has an analogy with the nonlocality test proposed by Banaszek and Wodkiewicz [Phys. Rev. Lett. 82, 2009 (1999)]. Our approach to deriving the classical bound draws on the fact that the Wigner function of a coherent state is a product of two independent distributions as if the orthogonal quadratures (position and momentum) in phase space behave as local realistic variables. Our method detects every pure nonclassical Gaussian state, which can also be extended to mixed states. Furthermore, it sets a bound for all Gaussian states and their mixtures, thereby providing a criterion to detect a genuine quantum non-Gaussian state. Remarkably, our phase-space approach with invariance under Gaussian unitary operations leads to an optimized test for a given non-Gaussian state. We experimentally show how this enhanced method can manifest quantum non-Gaussianity of a state by simply choosing phase-space points appropriately, which is essentially equivalent to implementing a squeezing operation on a given state.

quant-ph↗

arXiv2015

Impurity-induced bound states in superconductors with spin-orbit coupling

We study the effect of strong spin-orbit coupling (SOC) on bound states induced by impurities in superconductors. The presence of spin-orbit coupling breaks the $\mathbb{SU}(2)$-spin symmetry and causes the superconducting order parameter to have generically both singlet (s-wave) and triplet (p-wave) components. We find that in the presence of SOC the spectrum of Yu-Shiba-Rusinov (YSR) states is qualitatively different in s-wave and p-wave superconductor, a fact that can be used to identify the superconducting pairing symmetry of the host system. We also predict that in the presence of SOC the spectrum of the impurity-induced bound states depends on the orientation of the magnetic moment $\bf{S}$ of the impurity and, in particular, that by changing the orientation of $\bf{S}$ the fermion-parity of the lowest energy bound state can be tuned. We then study the case of a dimer of magnetic impurities and show that in this case the YSR spectrum for a p-wave superconductor is qualitatively very different from the one for an s-wave superconductor even in the limit of vanishing SOC. Our predictions can be used to distinguish the symmetry of the order parameter and have implications for the Majorana proposals based on chains of magnetic atoms placed on the surface of superconductors with strong spin-orbit coupling.

cond-mat.supr-con↗

arXiv2015

Potts model based on a Markov process computation solves the community structure problem effectively

Potts model is a powerful tool to uncover community structure in complex networks. Here, we propose a new framework to reveal the optimal number of communities and stability of network structure by quantitatively analyzing the dynamics of Potts model. Specifically we model the community structure detection Potts procedure by a Markov process, which has a clear mathematical explanation. Then we show that the local uniform behavior of spin values across multiple timescales in the representation of the Markov variables could naturally reveal the network's hierarchical community structure. In addition, critical topological information regarding to multivariate spin configuration could also be inferred from the spectral signatures of the Markov process. Finally an algorithm is developed to determine fuzzy communities based on the optimal number of communities and the stability across multiple timescales. The effectiveness and efficiency of our algorithm are theoretically analyzed as well as experimentally validated.

physics.soc-ph↗

arXiv2015

Identifying overlapping communities in social networks using multi-scale local information expansion

Most existing approaches for community detection require complete information of the graph in a specific scale, which is impractical for many social networks. We propose a novel algorithm that does not embrace the universal approach but instead of trying to focus on local social ties and modeling multi-scales of social interactions occurring in those networks. Our method for the first time optimizes the topological entropy of a network and uncovers communities through a novel dynamic system converging to a local minimum by simply updating the membership vector with very low computational complexity. It naturally supports overlapping communities through associating each node with a membership vector which describes node's involvement in each community. This way, in addition to uncover overlapping communities, we can also describe different multi-scale partitions by tuning the characteristic size of modules from the optimal partition. Because of the high efficiency and accuracy of the algorithm, it is feasible to be used for the accurate detection of community structure in real networks.

physics.soc-ph↗

arXiv2014

Disorder-tuned selection of order in bilayer graphene

The nature of the interaction-driven spontaneously broken-symmetry state in charge neutral bilayer graphene (BLG) has attracted a lot of interest. Theoretical studies predict various ordered states as the candidates for the ground state of BLG in the absence of external fields. Several experiments have been performed by different groups to identify the nature of the collective ground state in BLG. However, so far, there is no consensus: some experiments show evidence that suggests the establishment of a nematic gapless state, while others present results that are more consistent with the establishment of a fully gapped state. Moreover, even among the experiments that appear to see a bulk gap, some of the samples are found to be conducting (suggesting existence of gapless edge states), while others are insulating. Here we explore the hypothesis that disorder might explain the discrepancy between experiments. We find that the pair breaking effect due to non-magnetic short-range disorder varies among the candidate ground states, giving rise to different amounts of suppression of their mean-field transition temperatures. Our results indicate that BLG can undergo a transition between different ordered states as a function of the disorder strength providing a possible scenario to resolve the discrepancy between experimental observations.

cond-mat.mes-hall↗

arXiv2014

Experimental Test of Quantum Jarzynski Equality with a Trapped Ion System

The past two decades witnessed important developments in the field of non-equilibrium statistical mechanics. Among these developments, the Jarzynski equality, being a milestone following the landmark work of Clausius and Kelvin, stands out. The Jarzynski equality relates the free energy difference between two equilibrium states and the work done on the system through far from equilibrium processes. While experimental tests of the equality have been performed in classical regime, the verification of the quantum Jarzynski equality has not yet been fully demonstrated due to experimental challenges. Here, we report an experimental test of the quantum Jarzynski equality with a single \Yb ion trapped in a harmonic potential. We perform projective measurements to obtain phonon distributions of the initial thermal state. Following that we apply the laser induced force on the projected energy eigenstate, and find transition probabilities to final energy eigenstates after the work is done. By varying the speed of applying the force from equilibrium to far-from equilibrium regime, we verified the quantum Jarzynski equality in an isolated system.

quant-ph↗

arXiv2014

Time Reversal and Charge Conjugation in an Embedding Quantum Simulator

The understanding of symmetry operations has brought enormous advancements in physics, ranging from elementary particle to condensed matter systems. In quantum mechanics, symmetry operations are described by either unitary or antiunitary operators, where the latter are unphysical transformations that cannot be realized in physical systems. So far, quantum simulators of unitary and dissipative processes, the only allowed physical dynamics, have been realized in key experiments. Here, we present an embedding quantum simulator able to encode unphysical operations in a multilevel single trapped ion. In this sense, we experimentally observe phenomena associated with the nonunitary Majorana dynamics and implement antiunitary symmetry operations, i.e., time reversal and charge conjugation, at arbitrary evolution times. These experiments enhance the toolbox of quantum simulations towards applications involving unphysical operations.

quant-ph↗

arXiv2014

Proximity effect in graphene-topological insulator heterostructures

We formulate a continuum model to study the low-energy electronic structure of heterostructures formed by graphene on a strong three-dimensional topological insulator (TI) for the case of both commensurate and incommensurate stacking. The incommensurability can be due to a twist angle between graphene and the TI surface or a lattice mismatch between the two systems. We find that the proximity of the TI induces in graphene a strong enhancement of the spin-orbit coupling that can be tuned via the twist angle.

cond-mat.mes-hall↗

arXiv2013

Chiral superfluid states in hybrid graphene heterostructures

The use of high quality hexagonal boron nitride (hBN) as a dielectric material has made possible the realization of graphene devices with very high mobility. In addition hBN can be made as thin as few atomic layers and, as recently demonstrated experimentally, can be used to isolate electrically two graphene layers only few nanometers apart. The combined use of graphene and hBN has therefore opened the possibility to create novel electronic structures. In this work we study the "hybrid" heterostructure formed by one sheet of single layer graphene (SLG) and one sheet of bilayer graphene (BLG) separated by a thin film of hBN. In general it is expected that interlayer interactions can drive the system to a spontaneously broken symmetry state characterized by interlayer phase coherence. The peculiarity of the SLG-BLG heterostructure is that the electrons in the layers (SLG and BLG) have different chiralities. We find that the difference of chirality between electrons in the two layers causes the spontaneously broken symmetry state to be N-fold degenerate. Moreover, we find that some of the degenerate states are chiral superfluid states, topologically distinct from the usual layer-ferromagnetism. The chiral nature of the ground state opens the possibility to realize protected midgap states. The N-fold degeneracy of the ground state makes the physics of SLG-BLG hybrid systems analogous to the physics of helium-3, in particular given the recent discovery of chiral superfluid states in this system.

cond-mat.mes-hall↗

arXiv2013

Transient Charge and Energy Balance in Graphene Induced by Ultrafast Photoexcitation

Ultrafast optical pump-probe spectroscopy measurement on monolayer graphene observes significant optical nonlinearities. We show that strongly photoexcited graphene monolayers with 35 fs pulses quasi-instantaneously build up a broadband, inverted Dirac fermion population. Optical gain emerges and directly manifests itself via a negative conductivity at the near-infrared region for the first 200fs, where stimulated emission completely compensates absorption loss in the graphene layer. To quantitatively investigate this transient, extremely dense photoexcited Dirac-fermion state, we construct a two-chemical-potential model, in addition to a time-dependent transient carrier temperature above lattice temperature, to describe the population inverted electronic state metastable on the time scale of tens of femtoseconds generated by a strong exciting pulse. The calculated transient optical conductivity reveals a complete bleaching of absorption, which sets the saturation density during the pulse propagation. Particularly, the model calculation reproduces the negative optical conductivity at lower frequencies in the states close to saturation, corroborating the observed femtosecond stimulated emission and optical gain in the wide near-infrared window.

cond-mat.mes-hall↗

arXiv2013

Realization of Geometric Landau-Zener-Stückelberg Interferometry

We report the first experimental realization of the geometric Landau-Zener-Stückelberg (LZS) interferometry proposed by [Phys. Rev. Lett. 107, 207002 (2011)] in a single trapped ion system. Different from a conventional LZS interferometer, the interference fringes of our geometric interferometer originate solely from geometric phase. We also observe the robustness of the interference contrast against noise or fluctuation in the experimental parameters. Our scheme can be applied to other complex systems subject to relatively large errors in system control.

quant-ph↗