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Félix Mouhat, Sandro Sorella, Rodolphe Vuilleumier, Antonino Marco Saitta, Michele Casula
We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most advanced post Hartree-Fock approaches, and with a favorable scaling with the system size...
April 25, 2017: Journal of Chemical Theory and Computation
Yang Shin Park, Chang Hee Lee, Jeong Woo Kim, Young-Sun Lee, MunYoung Paek, Kyeong Ah Kim
PURPOSE: The aim of this study was to compare intraindividual single and multiple arterial phase acquisitions and evaluate which acquisition method was more advantageous for obtaining high-quality hepatic arterial phase in gadoxetic acid-enhanced liver magnetic resonance imaging (MRI). MATERIALS AND METHODS: Sixty-seven patients who underwent gadoxetic acid-enhanced liver MRIs and had all 3 kinds of acquisitions (single, dual, and triple arterial phases) were retrospectively included...
April 24, 2017: Investigative Radiology
Barbara Fresch, Francoise Remacle, Raphael D Levine
The implementation of probabilistic algorithms by deterministic hardware is demanding and requires hundreds of instructions to generate pseudo-random sequence of numbers. On the contrary, the dynamics at the molecular scale is physically governed by probabilistic laws because of the stochastic nature of thermally activated and quantum processes. By simulating the exciton transfer dynamics in a multi chromophoric system we demonstrate the implementation of a random walk that samples the possible pathways of a traveler through a network and can be probed by time resolved fluorescence spectroscopy...
April 25, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Junji Ito, Yukako Yamane, Mika Suzuki, Pedro Maldonado, Ichiro Fujita, Hiroshi Tamura, Sonja Grün
Previous studies have reported that humans employ ambient and focal modes of visual exploration while they freely view natural scenes. These two modes have been characterized based on eye movement parameters such as saccade amplitude and fixation duration, but not by any visual features of the viewed scenes. Here we propose a new characterization of eye movements during free viewing based on how eyes are moved from and to objects in a visual scene. We applied this characterization to data obtained from freely-viewing macaque monkeys...
April 24, 2017: Scientific Reports
G V S S Praneeth Varma, Rayapati Sushma, Vandana Sharma, Abhinav Kumar, G V V Sharma
In this paper, a simple heuristic power allocation scheme is proposed for a random LED array to obtain uniform irradiance on the projection surface. This is done by considering a binomial point process (BPP) for modeling the LED location and using the quality factor as a performance metric. Numerical results are provided to validate the proposed model and demonstrate its simplicity over existing LED geometries.
April 17, 2017: Optics Express
David M Holloway, Alexander V Spirov
Anterior-posterior (AP) body segmentation of the fruit fly (Drosophila) is first seen in the 7-stripe spatial expression patterns of the pair-rule genes, which regulate downstream genes determining specific segment identities. Regulation of pair-rule expression has been extensively studied for the even-skipped (eve) gene. Recent live imaging, of a reporter for the 2nd eve stripe, has demonstrated the stochastic nature of this process, with 'bursts' in the number of RNA transcripts being made over time. We developed a stochastic model of the spatial and temporal expression of eve stripe 2 (binding by transcriptional activators (Bicoid and Hunchback proteins) and repressors (Giant and Krüppel proteins), transcriptional initiation and termination; with all rate parameters constrained by features of the experimental data) in order to analyze the noisy experimental time series and test hypotheses for how eve transcription is regulated...
2017: PloS One
Daniele Ravi, Himar Fabelo, Gustavo Marrero Callico, GuangZhong Yang
Recent advances in hyperspectral imaging have made it a promising solution for intra-operative tissue characterization, with the advantages of being non-contact, non-ionizing and non-invasive. Working with hyperspectral images in vivo, however, is not straightforward as the high dimensionality of the data makes real-time processing challenging. In this paper, a novel dimensionality reduction scheme and a new processing pipeline are introduced to obtain a detailed tumour classification map for intra-operative margin definition during brain surgery...
April 24, 2017: IEEE Transactions on Medical Imaging
Bin Wang, Zhijian Ou, Zhiqiang Tan
To describe trans-dimensional observations in sample spaces of different dimensions, we propose a probabilistic model, called the trans-dimensional random field (TRF) by explicitly mixing a collection of random fields. In the framework of stochastic approximation (SA), we develop an effective training algorithm, called augmented SA, which jointly estimates the model parameters and normalizing constants while using trans-dimensional mixture sampling to generate observations of different dimensions. Furthermore, we introduce several statistical and computational techniques to improve the convergence of the training algorithm and reduce computational cost, which together enable us to successfully train TRF models on large datasets...
April 24, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
D M Halliday, J R Rosenberg
A comparison of previously defined spike train syncrhonization indices is undertaken within a stochastic point process framework. The second order cumulant density (covariance density) is shown to be common to all the indices. Simulation studies were used to investigate the sampling variability of a single index based on the second order cumulant. The simulations used a paired motoneurone model and a paired regular spiking cortical neurone model. The sampling variability of spike trains generated under identical conditions from the paired motoneurone model varied from 50% { 160% of the estimated value...
April 24, 2017: IEEE Transactions on Bio-medical Engineering
Andy R Eugene
OBJECTIVE: This article seeks to test the hypothesis that repeated 1mg intravenous epinephrine dosing intervals of 3-minutes and 5-minutes results in differences in the total drug exposure and the maximum epinephrine concentration using simulated cardiopulmonary resuscitation (CPR) dosing. METHODS: Published population pharmacokinetic parameters were identified in the literature and pharmacokinetic dosing simulations were conducted according to the 2015 American Heart Association guidelines for CPR in adults...
June 2016: MEDtube Science
Michael D Nunez, Joachim Vandekerckhove, Ramesh Srinivasan
Perceptual decision making can be accounted for by drift-diffusion models, a class of decision-making models that assume a stochastic accumulation of evidence on each trial. Fitting response time and accuracy to a drift-diffusion model produces evidence accumulation rate and non-decision time parameter estimates that reflect cognitive processes. Our goal is to elucidate the effect of attention on visual decision making. In this study, we show that measures of attention obtained from simultaneous EEG recordings can explain per-trial evidence accumulation rates and perceptual preprocessing times during a visual decision making task...
February 2017: Journal of Mathematical Psychology
Daniele Pedretti, K Ulrich Mayer, Roger D Beckie
In mining environmental applications, it is important to assess water quality from waste rock piles (WRPs) and estimate the likelihood of acid rock drainage (ARD) over time. The mineralogical heterogeneity of WRPs is a source of uncertainty in this assessment, undermining the reliability of traditional bulk indicators used in the industry. We focused in this work on the bulk neutralizing potential ratio (NPR), which is defined as the ratio of the content of non-acid-generating minerals (typically reactive carbonates such as calcite) to the content of potentially acid-generating minerals (typically sulfides such as pyrite)...
April 12, 2017: Journal of Contaminant Hydrology
Lívia D Audino, Stephen J Murphy, Ludimila Zambaldi, Julio Louzada, Liza S Comita
There is increasing recognition that community assembly theory can offer valuable insights for ecological restoration. We studied community assembly processes following tropical forest restoration efforts, using dung beetles (Scarabaeidae) as a focal taxon to investigate taxonomic and functional patterns of biodiversity recovery. We evaluated the relative importance of the local environment (i.e., canopy cover, understory cover, tree basal area, and soil texture), landscape context (i.e., habitat patch proximity and availability and percentage of surrounding area classified as natural forest or Eucalyptus spp...
April 23, 2017: Ecological Applications: a Publication of the Ecological Society of America
Irina Bashkirtseva, Lev Ryashko
A problem of the analysis of the noise-induced extinction in population models with Allee effect is considered. To clarify mechanisms of the extinction, we suggest a new technique combining an analysis of the geometry of attractors and their stochastic sensitivity. For the conceptual one-dimensional discrete Ricker-type model, on the base of the bifurcation analysis, deterministic persistence zones are constructed in the space of initial states and biological parameters. It is shown that the random environmental noise can contract, and even destroy these persistence zones...
April 19, 2017: Theoretical Population Biology
Steven M Goodreau, Eli S Rosenberg, Samuel M Jenness, Nicole Luisi, Sarah E Stansfield, Gregorio A Millett, Patrick S Sullivan
BACKGROUND: In the USA, men who have sex men (MSM) are at high risk for HIV, and black MSM have a substantially higher prevalence of infection than white MSM. We created a simulation model to assess the strength of existing hypotheses and data that account for these disparities. METHODS: We built a dynamic, stochastic, agent-based network model of black and white MSM aged 18-39 years in Atlanta, GA, USA, that incorporated race-specific individual and dyadic-level prevention and risk behaviours, network attributes, and care patterns...
April 18, 2017: Lancet HIV
Recep M Gorguluarslan, Seung-Kyum Choi, Christopher J Saldana
A methodology is proposed for uncertainty quantification and validation to accurately predict the mechanical response of lattice structures used in the design of scaffolds. Effective structural properties of the scaffolds are characterized using a developed multi-level stochastic upscaling process that propagates the quantified uncertainties at strut level to the lattice structure level. To obtain realistic simulation models for the stochastic upscaling process and minimize the experimental cost, high-resolution finite element models of individual struts were reconstructed from the micro-CT scan images of lattice structures which are fabricated by selective laser melting...
April 12, 2017: Journal of the Mechanical Behavior of Biomedical Materials
Vincent Raquin, Louis Lambrechts
Dengue virus (DENV) is an RNA virus transmitted among humans by mosquito vectors, mainly Aedes aegypti. DENV transmission requires viral dissemination from the mosquito midgut to the salivary glands. During this process the virus undergoes several population bottlenecks, which are stochastic reductions in population size that restrict intra-host viral genetic diversity and limit the efficiency of natural selection. Despite the implications for virus transmission and evolution, DENV replication in salivary glands has not been directly demonstrated...
April 18, 2017: Virology
A Chenu, M Beau, J Cao, A Del Campo
We introduce a scheme for the quantum simulation of many-body decoherence based on the unitary evolution of a stochastic Hamiltonian. Modulating the strength of the interactions with stochastic processes, we show that the noise-averaged density matrix simulates an effectively open dynamics governed by k-body Lindblad operators. Markovian dynamics can be accessed with white-noise fluctuations; non-Markovian dynamics requires colored noise. The time scale governing the fidelity decay under many-body decoherence is shown to scale as N^{-2k} with the system size N...
April 7, 2017: Physical Review Letters
Yan Qi Qin, B Normand, Anders W Sandvik, Zi Yang Meng
The amplitude ("Higgs") mode is a ubiquitous collective excitation related to spontaneous breaking of a continuous symmetry. We combine quantum Monte Carlo (QMC) simulations with stochastic analytic continuation to investigate the dynamics of the amplitude mode in a three-dimensional dimerized quantum spin system. We characterize this mode by calculating the spin and dimer spectral functions on both sides of the quantum critical point, finding that both the energies and the intrinsic widths of the excitations satisfy field-theoretical scaling predictions...
April 7, 2017: Physical Review Letters
Umberto Marini Bettolo Marconi, Andrea Puglisi, Claudio Maggi
Methods of stochastic thermodynamics and hydrodynamics are applied to a recently introduced model of active particles. The model consists of an overdamped particle subject to Gaussian coloured noise. Inspired by stochastic thermodynamics, we derive from the system's Fokker-Planck equation the average exchanges of heat and work with the active bath and the associated entropy production. We show that a Clausius inequality holds, with the local (non-uniform) temperature of the active bath replacing the uniform temperature usually encountered in equilibrium systems...
April 21, 2017: Scientific Reports
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