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Stochastic modeling

Ward Struyve
Loop quantum gravity is believed to eliminate singularities such as the big bang and big crunch singularity. This belief is based on studies of so-called loop quantum cosmology which concerns symmetry-reduced models of quantum gravity. In this paper, the problem of singularities is analysed in the context of the Bohmian formulation of loop quantum cosmology. In this formulation there is an actual metric in addition to the wave function, which evolves stochastically (rather than deterministically as the case of the particle evolution in non-relativistic Bohmian mechanics)...
August 15, 2017: Scientific Reports
Roilhi F Ibarra-Hernández, Miguel A Alonso-Arévalo, Alejandro Cruz-Gutiérrez, Ana L Licona-Chávez, Salvador Villarreal-Reyes
Heart sound analysis plays an important role in the auscultative diagnosis process to detect the presence of cardiovascular diseases. In this paper we propose a novel parametric heart sound model that accurately represents normal and pathological cardiac audio signals, also known as phonocardiograms (PCG). The proposed model considers that the PCG signal is formed by the sum of two parts: one of them is deterministic and the other one is stochastic. The first part contains most of the acoustic energy. This part is modeled by the Matching Pursuit (MP) algorithm, which performs an analysis-synthesis procedure to represent the PCG signal as a linear combination of elementary waveforms...
August 9, 2017: Computers in Biology and Medicine
Anna Ochab-Marcinek, Jakub Jędrak, Marcin Tabaka
An intuition based on deterministic models of chemical kinetics is that population heterogeneity of transcription factor levels in cells is transmitted unchanged downstream to the target genes. We use a stochastic model of a two-gene cascade with a self-regulating upstream gene to show that, counter to the intuition, there is no simple mapping (bimodal to bimodal, unimodal to unimodal) between the shapes of the distributions of transcription factor numbers and target protein numbers in cells. Due to the presence of the two regulations, the system contains two nonlinear transfer functions, defined by the Hill kinetics of transcription factor binding...
August 15, 2017: Physical Chemistry Chemical Physics: PCCP
Valérie Voorsluijs, Ioannis G Kevrekidis, Yannick De Decker
The photosensitive Belousov-Zhabotinsky (pBZ) reaction has been used extensively to study the properties of chemical oscillators. In particular, recent experiments revealed the existence of complex spatiotemporal dynamics for systems consisting of coupled micelles (V < 10(-21) L) or droplets (V ≈ [10(-8)-10(-11)] L) in which the pBZ reaction takes place. These results have been mostly understood in terms of reaction-diffusion models. However, in view of the small size of the droplets and micelles, large fluctuations of concentrations are to be expected...
August 15, 2017: Physical Chemistry Chemical Physics: PCCP
Zhuwen Li, Loong-Fah Cheong, Shuoguang Yang, Kim-Chuan Toh
While clustering has been well studied in the past decade, model selection has drawn much less attention due to the difficulty of the problem. In this paper, we address both problems in a joint manner by recovering an ideal affinity tensor from an imperfect input. By taking into account the relationship of the affinities induced by the cluster structures, we are able to significantly improve the affinity input, such as repairing those entries corrupted by gross outliers. More importantly, the recovered ideal affinity tensor also directly indicates the number of clusters and their membership, thus solving the model selection and clustering jointly...
August 14, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
Hossein Jashnsaz, Gregory G Anderson, Steve Pressé
Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena -- such as the volcano effect or banding -- have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources...
August 15, 2017: Physical Biology
Mauro César Cafundó Morais, Izabella Stuhl, Alan U Sabino, Willian W Lautenschlager, Alexandre S Queiroga, Tharcisio Citrangulo Tortelli, Roger Chammas, Yuri Suhov, Alexandre F Ramos
Contact inhibition is a central feature orchestrating cell proliferation in culture experiments; its loss is associated with malignant transformation and tumorigenesis. We performed a co-culture experiment with human metastatic melanoma cell line (SKMEL- 147) and immortalized keratinocyte cells (HaCaT). After 8 days a spatial pattern was detected, characterized by the formation of clusters of melanoma cells surrounded by keratinocytes constraining their proliferation. In addition, we observed that the proportion of melanoma cells within the total population has increased...
August 14, 2017: Scientific Reports
Marcelo Martins de Oliveira, Ronald Dickman
According to the competitive exclusion principle, in a finite ecosystem, extinction occurs naturally when two or more species compete for the same resources. An important question that arises is: when coexistence is not possible, which mechanisms confer an advantage to a given species against the other(s)? In general, it is expected that the species with the higher reproductive/death ratio will win the competition, but other mechanisms, such as asymmetry in interspecific competition or unequal diffusion rates, have been found to change this scenario dramatically...
2017: PloS One
S Sekiguchi, P Presi, R Omori, K Staerk, M Schuppers, N Isoda, Y Yoshikawa, T Umemura, H Nakayama, Y Fujii, Y Sakoda
Bovine viral diarrhoea virus (BVDV) infection in cattle can result in growth retardation, reduced milk production, reproductive disorders and death. Persistently infected animals are the primary source of infection. In Hokkaido, Japan, all cattle entering shared pastures in summer are vaccinated before movement for disease control. Additionally, these cattle may be tested for BVDV and culled if positive. However, the effectiveness of this control strategy aiming to reduce the number of BVDV-infected animals has not been assessed...
August 14, 2017: Transboundary and Emerging Diseases
Siting Gan, Erin K O'Shea
The endogenous circadian clock synchronizes with environmental time by appropriately resetting its phase in response to external cues. Of note, some resetting stimuli induce attenuated oscillations of clock output, which has been observed at the population-level in several organisms and in studies of individual humans. To investigate what is happening in individual cellular clocks, we studied the unicellular cyanobacterium S. elongatus. By measuring its phase-resetting responses to temperature changes, we found that population-level arrhythmicity occurs when certain perturbations cause stochastic phases of oscillations in individual cells...
August 9, 2017: Molecular Cell
Monika Scholz, Aaron R Dinner, Erel Levine, David Biron
Animals regulate their food intake in response to the available level of food. Recent observations of feeding dynamics in small animals showed feeding patterns of bursts and pauses, but their function is unknown. Here, we present a data-driven decision-theoretical model of feeding in Caenorhabditis elegans Our central assumption is that food intake serves a dual purpose: to gather information about the external food level and to ingest food when the conditions are good. The model recapitulates experimentally observed feeding patterns...
August 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
Stefanie Winkelmann, Christof Schütte
Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest. We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments, and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method...
December 7, 2016: Journal of Chemical Physics
Yong Han, Maozhi Li, James W Evans
A fundamental evolution equation is developed to describe the distribution of areas of capture zones (CZs) associated with islands formed by homogeneous nucleation and growth during submonolayer deposition on perfect flat surfaces. This equation involves various quantities which characterize subtle spatial aspects of the nucleation process. These quantities in turn depend on the complex stochastic geometry of the CZ tessellation of the surface, and their detailed form determines the CZ area distribution (CZD) including its asymptotic features...
December 7, 2016: Journal of Chemical Physics
Ling Lan, Dipankar Bandyopadhyay, Somnath Datta
Datasets examining periodontal disease records current (disease) status information of tooth-sites, whose stochastic behavior can be attributed to a multistate system with state occupation determined at a single inspection time. In addition, the tooth-sites remain clustered within a subject, and the number of available tooth-sites may be representative of the true PD status of that subject, leading to an 'informative cluster size' scenario. To provide insulation against incorrect model assumptions, we propose a nonparametric regression framework to estimate state occupation probabilities at a given time and state exit/entry distributions, utilizing weighted monotonic regression and smoothing techniques...
January 2017: Statistica Neerlandica
Inés P Mariño, Alexey Zaikin, Joaquín Míguez
We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model...
2017: PloS One
Diana María Herrera-Ibatá, Beatriz Martínez-López, Darla Quijada, Kenneth Burton, Lina Mur
The US livestock safety strongly depends on its capacity to prevent the introduction of Transboundary Animal Diseases (TADs). Therefore, accurate and updated information on the location and origin of those potential TADs risks is essential, so preventive measures as market restrictions can be put on place. The objective of the present study was to evaluate the current risk of African swine fever (ASF) and Classical swine fever (CSF) introduction into the US through the legal importations of live pigs and swine products using a quantitative approach that could be later applied to other risks...
2017: PloS One
Thomas A A Prowse, Phillip Cassey, Joshua V Ross, Chandran Pfitzner, Talia A Wittmann, Paul Thomas
Self-replicating gene drives that can spread deleterious alleles through animal populations have been promoted as a much needed but controversial 'silver bullet' for controlling invasive alien species. Homing-based drives comprise an endonuclease and a guide RNA (gRNA) that are replicated during meiosis via homologous recombination. However, their efficacy for controlling wild populations is threatened by inherent polymorphic resistance and the creation of resistance alleles via non-homologous end-joining (NHEJ)-mediated DNA repair...
August 16, 2017: Proceedings. Biological Sciences
Eric Charles Dykeman
Previously, a stochastic model of single-stranded RNA virus assembly was created to model the cooperative effects between capsid proteins and genomic RNA that would occur in a packaging signal-mediated assembly process. In such an assembly scenario, multiple secondary structural elements from within the RNA, termed "packaging signals" (PS), contact coat proteins and facilitate efficient capsid assembly. In this work, the assembly model is extended to incorporate explicit nucleotide sequence information as well as simple aspects of RNA folding that would be occurring during the RNA/capsid coassembly process...
August 8, 2017: Biophysical Journal
Khadija Yazda, Saïd Tahir, Thierry Michel, Bastien Loubet, Manoel Manghi, Jeremy Bentin, Fabien Picaud, John Palmeri, François Henn, Vincent Jourdain
Ionic transport through single-walled carbon nanotubes (SWCNTs) is promising for many applications but remains both experimentally challenging and highly debated. Here we report ionic current measurements through microfluidic devices containing one or several SWCNTs of diameter of 1.2 to 2 nm unexpectedly showing a linear or a voltage-activated I-V dependence. Transition from an activated to a linear behavior, and stochastic fluctuations between different current levels were notably observed. For linear devices, the high conductance confirmed with different chloride salts indicates that the nanotube/water interface exhibits both a high surface charge density and flow slippage, in agreement with previous reports...
August 9, 2017: Nanoscale
Markus Ableidinger, Evelyn Buckwar, Harald Hinterleitner
Neural mass models provide a useful framework for modelling mesoscopic neural dynamics and in this article we consider the Jansen and Rit neural mass model (JR-NMM). We formulate a stochastic version of it which arises by incorporating random input and has the structure of a damped stochastic Hamiltonian system with nonlinear displacement. We then investigate path properties and moment bounds of the model. Moreover, we study the asymptotic behaviour of the model and provide long-time stability results by establishing the geometric ergodicity of the system, which means that the system-independently of the initial values-always converges to an invariant measure...
August 8, 2017: Journal of Mathematical Neuroscience
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