Realistic simulations of single-spin nondemolition measurement by magnetic resonance force microscopy

A requirement for many quantum computation schemes is the ability to measure single spins. This paper examines one proposed scheme: magnetic resonance force microscopy, including the effects of thermal noise and back-action from monitoring. We derive a simplified equation using the adiabatic approximation, and produce a stochastic pure state unraveling which is useful for numerical simulations.Comment: 33 pages LaTeX, 9 figure files in EPS format. Submitted to Physical Review

Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Molecular dynamics study of accelerated ion-induced shock waves in biological media

We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model

Quantum central limit theorem for continuous-time quantum walks on odd graphs in quantum probability theory

The method of the quantum probability theory only requires simple structural data of graph and allows us to avoid a heavy combinational argument often necessary to obtain full description of spectrum of the adjacency matrix. In the present paper, by using the idea of calculation of the probability amplitudes for continuous-time quantum walk in terms of the quantum probability theory, we investigate quantum central limit theorem for continuous-time quantum walks on odd graphs.Comment: 19 page, 1 figure

Universality of the Lyapunov regime for the Loschmidt echo

The Loschmidt echo (LE) is a magnitude that measures the sensitivity of quantum dynamics to perturbations in the Hamiltonian. For a certain regime of the parameters, the LE decays exponentially with a rate given by the Lyapunov exponent of the underlying classically chaotic system. We develop a semiclassical theory, supported by numerical results in a Lorentz gas model, which allows us to establish and characterize the universality of this Lyapunov regime. In particular, the universality is evidenced by the semiclassical limit of the Fermi wavelength going to zero, the behavior for times longer than Ehrenfest time, the insensitivity with respect to the form of the perturbation and the behavior of individual (non-averaged) initial conditions. Finally, by elaborating a semiclassical approximation to the Wigner function, we are able to distinguish between classical and quantum origin for the different terms of the LE. This approach renders an understanding for the persistence of the Lyapunov regime after the Ehrenfest time, as well as a reinterpretation of our results in terms of the quantum--classical transition.Comment: 33 pages, 17 figures, uses Revtex

Dynamical aspects of quantum entanglement for weakly coupled kicked tops

We investigate how the dynamical production of quantum entanglement for weakly coupled, composite quantum systems is influenced by the chaotic dynamics of the corresponding classical system, using coupled kicked tops. The linear entropy for the subsystem (a kicked top) is employed as a measure of entanglement. A perturbative formula for the entanglement production rate is derived. The formula contains a correlation function that can be evaluated only from the information of uncoupled tops. Using this expression and the assumption that the correlation function decays exponentially which is plausible for chaotic tops, it is shown that {\it the increment of the strength of chaos does not enhance the production rate of entanglement} when the coupling is weak enough and the subsystems (kicked tops) are strongly chaotic. The result is confirmed by numerical experiments. The perturbative approach is also applied to a weakly chaotic region, where tori and chaotic sea coexist in the corresponding classical phase space, to reexamine a recent numerical study that suggests an intimate relationship between the linear stability of the corresponding classical trajectory and the entanglement production rate.Comment: 16 pages, 11 figures, submitted to Phys. Rev.

Towards Reliable Automatic Protein Structure Alignment

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based on local structure similarity. In this work, we propose a method to incorporate global information in obtaining optimal alignments and superpositions. Our method, when applied to optimizing the TM-score and the GDT score, produces significantly better results than current state-of-the-art protein structure alignment tools. Specifically, if the highest TM-score found by TMalign is lower than (0.6) and the highest TM-score found by one of the tested methods is higher than (0.5), there is a probability of (42%) that TMalign failed to find TM-scores higher than (0.5), while the same probability is reduced to (2%) if our method is used. This could significantly improve the accuracy of fold detection if the cutoff TM-score of (0.5) is used. In addition, existing structure alignment algorithms focus on structure similarity alone and simply ignore other important similarities, such as sequence similarity. Our approach has the capacity to incorporate multiple similarities into the scoring function. Results show that sequence similarity aids in finding high quality protein structure alignments that are more consistent with eye-examined alignments in HOMSTRAD. Even when structure similarity itself fails to find alignments with any consistency with eye-examined alignments, our method remains capable of finding alignments highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Determination of trace elements in natural water samples by air-segmented flow-injection/ICP-MS after preconcentration with a chitosan-based chelating resin

本法では,各種天然水中の極微量金属成分を同時定量する目的で空気分節試料導入/ICP-MSシステムを用いて,微少量試料(数十μl)を前処理せずにネブライザーに送り込み,多数の金属成分の定量が可能であった。共存主成分による質量干渉を受ける一部遷移金属や直接試料導入では感度の足りない元素については,イミノ二酢酸型キトサンキレート樹脂充填カラムによる分離·濃縮操作の併用によって更に信頼性の高いデータが得られることが分かった。前処理においては,体積1mlのミニカラムを用いて50mlの溶液試料から50倍濃縮を行い,試料·試薬·廃液すべてを少量化することができた。本ICP-MSシステムでは試料導入量は80μlで十分であり,1mlでも数回繰り返し測定が可能で,しかも多元素同時分析ができた。確立した分析法を用いて河川水や市販のミネラルウォーターに応用し,希土類を含め45種の微量元素の定量が可能となった。Ultratrace elements in natural water samples were determined simultaneously by air-segmented flow-injection/inductively coupled plasma-mass spectrometry(SFI/ICP-MS).A small volume of the sample solutions(80μl) was introduced into a nebulizer by an air-segmented flow-injection(SFI) system, and a maximum of fifteen elements were measured during each run.A chitosan-based chelating resin containing functional groups of iminodiacetate was used to separate and enrich analyte metal ions.A 50-fold preconcentration using 50ml of sample solutions was achieved by the proposed method, where 1ml of 0.1M nitric acid was added to residues after drying the chelating column effluent.At pH6, several heavy metals(Fe, Ni, Co, Cu, Zn, Ag, Cd, Pb and U) and rare earth elements(REEs) were quantitatively retained on the chelating resin column, whereas alkali and alkaline earth metals were eluted from the column by rinsing with 5ml of a 0.2M ammonium acetate solution.Metals adsorbed on the chelating resin column were recovered by elution with 10ml of 1M nitric acid.The proposed method was applied to the determination of trace elements in several natural water samples, such as river water and mineral drinking water

Discrete molecular dynamics simulations of peptide aggregation

We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet structure. This structure has an inter-strand distance of 0.48 nm and an inter-sheet distance of 1.0 nm, which agree with experimental observations. In this model, the hydrogen bond interactions give rise to the inter-strand spacing in beta-sheets, while the Go interactions among side chains make beta-strands parallel to each other and allow beta-sheets to pack into layers. The aggregates also contain free edges which may allow for further aggregation of model peptides to form elongated fibrils.Comment: 15 pages, 8 figure