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https://www.readbyqxmd.com/read/28531219/pyldm-an-open-source-package-for-lifetime-density-analysis-of-time-resolved-spectroscopic-data
#1
Gabriel F Dorlhiac, Clyde Fare, Jasper J van Thor
Ultrafast spectroscopy offers temporal resolution for probing processes in the femto- and picosecond regimes. This has allowed for investigation of energy and charge transfer in numerous photoactive compounds and complexes. However, analysis of the resultant data can be complicated, particularly in more complex biological systems, such as photosystems. Historically, the dual approach of global analysis and target modelling has been used to elucidate kinetic descriptions of the system, and the identity of transient species respectively...
May 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28530285/one-step-formulation-of-nonionic-surfactant-bicelles-nsbs-by-a-double-tailed-polyglycerol-type-nonionic-surfactant
#2
Kenji Aramaki, Chikahiro Iwata, Jitendra Mata, Tetsuya Maehara, Daisuke Aburano, Yuichi Sakanishi, Kyuhei Kitao
Bicelles are generally formed by phospholipid-based systems and are useful for various applications, such as nanocarriers or membrane protein crystallization. The same disc-like assemblies, nonionic surfactant bicelles (NSBs), can also be formed using nonionic amphiphiles, but this has not been reported extensively. We report a novel NSB system that employs the double-tailed nonionic amphiphile, polyglyceryl dialkyl ether (C12CmGn), which has two alkyl chains and a polyglyceryl group. A symmetric-tail molecule, C12C12G13...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530269/a-critical-comparison-of-coarse-grained-structure-based-approaches-and-atomic-models-of-protein-folding
#3
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530167/biofilm-community-succession-a-neutral-perspective
#4
Stephen Woodcock, William T Sloan
Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested...
May 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28529671/the-advection-of-microparticles-mcf-7-and-mda-mb-231-breast-cancer-cells-in-response-to-very-low-reynolds-numbers
#5
Sinéad T Morley, Michael T Walsh, David T Newport
The lymphatic system is an extensive vascular network that serves as the primary route for the metastatic spread of breast cancer cells (BCCs). The dynamics by which BCCs travel in the lymphatics to distant sites, and eventually establish metastatic tumors, remain poorly understood. Particle tracking techniques were employed to analyze the behavior of MCF-7 and MDA-MB-231 BCCs which were exposed to lymphatic flow conditions in a 100 μm square microchannel. The behavior of the BCCs was compared to rigid particles of various diameters (η = dp/H= 0...
May 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28529154/habitat-heterogeneity-hypothesis-and-edge-effects-in-model-metacommunities-marked-manuscript
#6
Michaela Hamm, Barbara Drossel
Spatial heterogeneity is an inherent property of any living environment and is expected to favour biodiversity due to a broader niche space. Furthermore, edges between different habitats can provide additional possibilities for species coexistence. Using computer simulations, this study examines metacommunities consisting of several trophic levels in heterogeneous environments in order to explore the above hypotheses on a community level. We model heterogeneous landscapes by using two different sized resource pools and evaluate the combined effect of dispersal and heterogeneity on local and regional species diversity...
May 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28529153/model-of-vascular-desmoplastic-multispecies-tumor-growth
#7
Chin F Ng, Hermann B Frieboes
We present a three-dimensional nonlinear tumor growth model composed of heterogeneous cell types in a multicomponent-multispecies system, including viable, dead, healthy host, and extra-cellular matrix (ECM) tissue species. The model includes the capability for abnormal ECM dynamics noted in tumor development, as exemplified by pancreatic ductal adenocarcinoma, including dense desmoplasia typically characterized by a significant increase of interstitial connective tissue. An elastic energy is implemented to provide elasticity to the connective tissue...
May 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28529143/dynamics-analysis-of-a-delayed-reaction-diffusion-predator-prey-system-with-non-continuous-threshold-harvesting
#8
Xuebing Zhang, Hongyong Zhao
This paper deals with a delayed reaction-diffusion predator-prey model with non-continuous threshold harvesting. Sufficient conditions for the local stability of the regular equilibrium, the existence of Hopf bifurcation and Turing bifurcation are obtained by analyzing the associated characteristic equation. By utilizing upper-lower solution method and Lyapunov functions the globally asymptotically stability of a unique regular equilibrium and asymptotically stability of a unique pseudoequilibrium are studied respectively...
May 18, 2017: Mathematical Biosciences
https://www.readbyqxmd.com/read/28529063/methodologies-for-studying-the-spliceosome-s-rna-dynamics-with-single-molecule-fret
#9
REVIEW
Clarisse van der Feltz, Aaron A Hoskins
The spliceosome is an extraordinarily dynamic molecular machine in which significant changes in composition as well as protein and RNA conformation are required for carrying out pre-mRNA splicing. Single-molecule fluorescence resonance energy transfer (smFRET) can be used to elucidate these dynamics both in well-characterized model systems and in entire spliceosomes. These types of single-molecule data provide novel information about spliceosome components and can be used to identify sub-populations of molecules with unique behaviors...
May 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28528863/cross-linking-of-a-biopolymer-peptide-co-assembling-system
#10
Karla E Inostroza-Brito, Estelle C Collin, Anna Poliniewicz, Sherif Elsharkawy, Alistair Rice, Armando E Del Río Hernández, Xin Xiao, José Rodríguez-Cabello, Alvaro Mata
The ability to guide molecular self-assembly at the nanoscale into complex macroscopic structures could enable the development of functional synthetic materials that exhibit properties of natural tissues such as hierarchy, adaptability, and self-healing. However, the stability and structural integrity of these kinds of materials remains a challenge for many practical applications. We have recently developed a dynamic biopolymer-peptide co-assembly system with the capacity to grow and undergo morphogenesis into complex shapes...
May 18, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28528699/steps-toward-maturation-of-embryonic-stem-cell-derived-cardiomyocytes-by-defined-physical-signals
#11
Nian Shen, Anne Knopf, Claas Westendorf, Udo Kraushaar, Julia Riedl, Hannah Bauer, Simone Pöschel, Shannon Lee Layland, Monika Holeiter, Stefan Knolle, Eva Brauchle, Ali Nsair, Svenja Hinderer, Katja Schenke-Layland
Cardiovascular disease remains a leading cause of mortality and morbidity worldwide. Embryonic stem cell-derived cardiomyocytes (ESC-CMs) may offer significant advances in creating in vitro cardiac tissues for disease modeling, drug testing, and elucidating developmental processes; however, the induction of ESCs to a more adult-like CM phenotype remains challenging. In this study, we developed a bioreactor system to employ pulsatile flow (1.48 mL/min), cyclic strain (5%), and extended culture time to improve the maturation of murine and human ESC-CMs...
May 18, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28528256/evaluation-of-artificial-time-series-microarray-data-for-dynamic-gene-regulatory-network-inference
#12
P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28528137/fuzzy-dynamic-output-feedback-h%C3%A2-control-for-continuous-time-t-s-fuzzy-systems-under-imperfect-premise-matching
#13
Tao Zhao, Songyi Dian
This paper addresses a fuzzy dynamic output feedback H∞ control design problem for continuous-time nonlinear systems via T-S fuzzy model. The stability of the fuzzy closed-loop system which is formed by a T-S fuzzy model and a fuProd. Type: FTPzzy dynamic output feedback H∞ controller connected in a closed loop is investigated with Lyapunov stability theory. The proposed fuzzy controller does not share the same membership functions and number of rules with T-S fuzzy systems, which can enhance design flexibility...
May 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28528112/microencapsulation-and-characterization-of-liposomal-vesicles-using-a-supercritical-fluid-process-coupled-with-vacuum-driven-cargo-loading
#14
Wen-Chyan Tsai, Syed S H Rizvi
A new technique of liposomal microencapsulation, consisting of supercritical fluid extraction followed by rapid expansion of the supercritical solution and vacuum-driven cargo loading, was successfully developed. It is a continuous flow-through process without usage of any toxic organic solvent. For use as a coating material, the solubility of soy phospholipids in supercritical carbon dioxide was first determined using a dynamic equilibrium system and the data was correlated with the Chrastil model with good agreement...
June 2017: Food Research International
https://www.readbyqxmd.com/read/28527468/insight-into-electric-field-induced-rupture-mechanism-of-water-in-toluene-emulsion-films-from-a-model-system
#15
Desislava Dimova, Stoyan Pisov, Nikolay Panchev, Miroslava Nedyalkova, Sergio Madurga, Ana Proykova
This paper presents a model, which we have designed to get insight into the development of electro-induced instability of a thin toluene emulsion film in contact with the saline aqueous phase. Molecular dynamics (MD) simulations demonstrate the role of charge accumulation in the toluene-film rupture induced by a DC electric field. Two ensembles-NVT and NPT-are used to determine the critical value of the external field at which the film ruptures, the charge distribution and capacitance of the thin film, number densities, and the film structure...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527452/structural-and-dynamic-inhomogeneities-induced-by-curvature-gradients-in-elliptic-colloidal-halos-of-paramagnetic-particles
#16
O A Ramírez-Garza, J M Méndez-Alcaraz, P González-Mozuelos
Paramagnetic colloidal particles distributed along an ellipse are used as a model system to study the effects of curvature gradients on the structure and dynamics of colloids in curved manifolds. Unlike what happens for circular and spherical systems, in the present case, the equilibrium one-particle distribution function displays inhomogeneities due to the changing curvature along the ellipse. The ensuing effects on the two-body correlations are also analyzed, leading to the observation of anisotropic and long-ranged effects...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527449/correlated-matrix-fluctuation-mediated-activated-transport-of-dilute-penetrants-in-glass-forming-liquids-and-suspensions
#17
Rui Zhang, Kenneth S Schweizer
We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527433/partial-hydrodynamic-representation-of-quantum-molecular-dynamics
#18
Bing Gu, Ignacio Franco
A hybrid method is proposed to propagate system-bath quantum dynamics that use both basis functions and coupled quantum trajectories. In it, the bath is represented with an ensemble of Bohmian trajectories while the system degrees of freedom are accounted through reduced density matrices. By retaining the Hilbert space structure for the system, the method is able to capture interference processes that are challenging to describe in Bohmian dynamics due to singularities that these processes introduce in the quantum potential...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527389/dynamics-of-dissolved-organic-matter-in-riverine-sediments-affected-by-weir-impoundments-production-benthic-flux-and-environmental-implications
#19
Meilian Chen, Sung-Han Kim, Heon-Jae Jung, Jung-Ho Hyun, Jung Hyun Choi, Hyo-Jin Lee, In-Ae Huh, Jin Hur
In order to understand the characteristics and dynamics of dissolved organic matter (DOM) in the sediment of rivers affected by impoundments, we examined the vertical profiles and the benthic fluxes of DOM in four different core sediments located at upstream sites of weirs in major rivers of South Korea. In three out of four sites, exponential accumulation of dissolved organic carbon (DOC) with depth was observed with the signature of seasonal variability. Except for the site displaying a below-detection limit of Fe(II), the general accumulation trends of DOC with depth was concurrent with the increases of Fe(II) and NH4(+) and the decrease of PO4(3-), signifying a close linkage of the DOM dynamics with anaerobic respiration via iron reduction, an important early diagenesis pathway...
May 12, 2017: Water Research
https://www.readbyqxmd.com/read/28526790/post-epizootic-persistence-of-asymptomatic-mycoplasma-conjunctivae-infection-in-iberian-ibex
#20
Xavier Fernández-Aguilar, Oscar Cabezón, José Enrique Granados, Joachim Frey, Emmanuel Serrano, Roser Velarde, Francisco Javier Cano-Manuel, Gregorio Mentaberre, Arián Ráez-Bravo, Paulino Fandos, Jorge Ramón López-Olvera
The susceptibility of Iberian ibex (Capra pyrenaica) to Mycoplasma conjunctivae ocular infection and the changes in their interaction over time were studied in terms of clinical outcome, molecular detection and IgG immune response in a captive population that underwent a severe infectious keratoconjunctivitis (IKC) outbreak. Mycoplasma conjunctivae was detected for the first time in the Iberian ibexes coinciding with the IKC outbreak. Its prevalence had a decreasing trend in 2013 that was consistent with the clinical resolution (August 35...
May 19, 2017: Applied and Environmental Microbiology
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