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Systems Dynamics

Florent Xavier Smit, Jurriaan A Luiken, Peter G Bolhuis
We performed replica exchange molecular dynamics and forward flux sampling simulations of hexapeptide VQIINK and VQIVYK systems, also known as, respectively, fragments PHF6* and PHF6 from tau protein. Part of the microtubule binding region, these fragments are known to be aggregation prone, and at least one of them is a prerequisite for fibril formation of the tau protein. Using a coarse-grained force field, we establish the phase behavior of both fragments, and investigate the nucleation kinetics for the conversion into a β-sheet fibril...
October 24, 2016: Journal of Physical Chemistry. B
Zahra Aghili, Saba Taheri, Hojjat Alizadeh Zeinabad, Leila Pishkar, Ali Akbar Saboury, Arash Rahimi, Mojtaba Falahati
Herein, the interaction of hen egg white lysozyme (HEWL) with iron nanoparticle (Fe NP) was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV) to HEWL (8.57±0.54 mV) can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV). In addition, dynamic light scattering (DLS) study revealed that addition of Fe NP (92.95±6.11 nm) to HEWL (2.68±0.37 nm) increases suspension potential of protein/nanoparticle system (51...
2016: PloS One
Yuchen Gao, Xin Xiong, Spencer Wong, Emeric J Charles, Wendell A Lim, Lei S Qi
The ability to dynamically manipulate the transcriptome is important for studying how gene networks direct cellular functions and how network perturbations cause disease. Nuclease-dead CRISPR-dCas9 transcriptional regulators, while offering an approach for controlling individual gene expression, remain incapable of dynamically coordinating complex transcriptional events. Here, we describe a flexible dCas9-based platform for chemical-inducible complex gene regulation. From a screen of chemical- and light-inducible dimerization systems, we identified two potent chemical inducers that mediate efficient gene activation and repression in mammalian cells...
October 24, 2016: Nature Methods
Matthias Kohl, Andreas Härtel, Michael Schmiedeberg
The slow dynamics in a glassy hard-sphere system is dominated by cage breaking events, i.e. rearrangements where a particle escapes from the cage formed by its neighboring particles. We study such events for an overdamped colloidal system by the means of Brownian dynamics simulations. While it is difficult to relate cage breaking events to structural mean field results in bulk, we show that the microscopic dynamics of particles close to a wall can be related to the anisotropic two-particle density. In particular, we study cage-breaking trajectories, mean forces on a tracked particle, and the impact of the history of trajectories...
October 24, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Wei-Lin Jin, Xiao-Yuan Mao, Guan-Zhong Qiu
Glioblastoma (GBM) is regarded as the most common primary intracranial neoplasm. Despite standard treatment with tumor resection and radiochemotherapy, the outcome remains gloomy. It is evident that a combination of oncogenic gain of function and tumor-suppressive loss of function has been attributed to glioma initiation and progression. The ubiquitin-proteasome system is a well-orchestrated system that controls the fate of most proteins by striking a dynamic balance between ubiquitination and deubiquitination of substrates, having a profound influence on the modulation of oncoproteins, tumor suppressors, and cellular signaling pathways...
October 24, 2016: Medicinal Research Reviews
Tae Soup Shim, Zaki G Estephan, Zhaoxia Qian, Jacob H Prosser, Su Yeon Lee, David M Chenoweth, Daeyeon Lee, So-Jung Park, John C Crocker
Active materials that respond to physical and chemical stimuli can be used to build dynamic micromachines that lie at the interface between biological systems and engineered devices. In principle, the specific hybridization of DNA can be used to form a library of independent, chemically driven actuators for use in such microrobotic applications and could lead to device capabilities that are not possible with polymer- or metal-layer-based approaches. Here, we report shape changing films that are powered by DNA strand exchange reactions with two different domains that can respond to distinct chemical signals...
October 24, 2016: Nature Nanotechnology
Yiming Zhao, Nong Zhang, Guangyao Si
Monitoring of roof activity is a primary measure adopted in the prevention of roof collapse accidents and functions to optimize and support the design of roadways in underground coalmines. However, traditional monitoring measures, such as using mechanical extensometers or electronic gauges, either require arduous underground labor or cannot function properly in the harsh underground environment. Therefore, in this paper, in order to break through this technological barrier, a novel monitoring system for roof safety control in underground coal mining, using fiber Bragg grating (FBG) material as a perceived element and transmission medium, has been developed...
October 21, 2016: Sensors
Melanie E M Stamp, Anna M Jötten, Patrick W Kudella, Dominik Breyer, Florian G Strobl, Thomas M Geislinger, Achim Wixforth, Christoph Westerhausen
Cell adhesion processes are of ubiquitous importance for biomedical applications such as optimization of implant materials. Here, not only physiological conditions such as temperature or pH, but also topographical structures play crucial roles, as inflammatory reactions after surgery can diminish osseointegration. In this study, we systematically investigate cell adhesion under static, dynamic and physiologically relevant conditions employing a lab-on-a-chip system. We screen adhesion of the bone osteosarcoma cell line SaOs-2 on a titanium implant material for pH and temperature values in the physiological range and beyond, to explore the limits of cell adhesion, e...
October 21, 2016: Diagnostics
Yu Gu, Yang-Fu Wang, Qiang Li, Zu-Wu Liu
Chinese liquors can be classified according to their flavor types. Accurate identification of Chinese liquor flavors is not always possible through professional sommeliers' subjective assessment. A novel polymer piezoelectric sensor electric nose (e-nose) can be applied to distinguish Chinese liquors because of its excellent ability in imitating human senses by using sensor arrays and pattern recognition systems. The sensor, based on the quartz crystal microbalance (QCM) principle is comprised of a quartz piezoelectric crystal plate sandwiched between two specific gas-sensitive polymer coatings...
October 20, 2016: Sensors
Qichao Zhang, Dongbin Zhao, Ding Wang
In this paper, the robust control problem for a class of continuous-time nonlinear system with unmatched uncertainties is investigated using an event-based control method. First, the robust control problem is transformed into a corresponding optimal control problem with an augmented control and an appropriate cost function. Under the event-based mechanism, we prove that the solution of the optimal control problem can asymptotically stabilize the uncertain system with an adaptive triggering condition. That is, the designed event-based controller is robust to the original uncertain system...
October 18, 2016: IEEE Transactions on Neural Networks and Learning Systems
Marta Franceschi, Lucia Seminara, Strahinja Dosen, Matjia Strbac, Maurizio Valle, Dario Farina
Myoelectric prostheses are successfully controlled using muscle electrical activity, thereby restoring lost motor functions. However, the somatosensory feedback from the prosthesis to the user is still missing. The sensory substitution methods described in the literature comprise mostly simple position and force sensors combined with discrete stimulation units. The present study describes a novel system for sophisticated electrotactile feedback integrating advanced distributed sensing (electronic skin) and stimulation (matrix electrodes)...
October 19, 2016: IEEE Transactions on Haptics
Joseph Lucisano, Timothy Routh, Joe Lin, David Gough
OBJECTIVE: The use of a fully implanted, first-generation prototype sensor/telemetry system is described for long-term monitoring of subcutaneous tissue glucose in a small cohort of people with diabetes. METHODS: Sensors are based on a membrane containing immobilized glucose oxidase and catalase coupled to electrochemical oxygen detection and telemetry systems, integrated as an implant. The devices remained implanted for up to 180 days, with signals transmitted every 2 minutes to external receivers...
October 19, 2016: IEEE Transactions on Bio-medical Engineering
Andreas Widder, Christian Kuehn
In this paper, we focus on the influence of heterogeneity and stochasticity of the population on the dynamical structure of a basic susceptible-infected-susceptible (SIS) model. First we prove that, upon a suitable mathematical reformulation of the basic reproduction number, the homogeneous system and the heterogeneous system exhibit a completely analogous global behaviour. Then we consider noise terms to incorporate the fluctuation effects and the random import of the disease into the population and analyse the influence of heterogeneity on warning signs for critical transitions (or tipping points)...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
K E Starkov, Svetlana Bunimovich-Mendrazitsky
Understanding the global interaction dynamics between tumor and the immune system plays a key role in the advancement of cancer therapy. Bunimovich-Mendrazitsky et al. (2015) developed a mathematical model for the study of the immune system response to combined therapy for bladder cancer with Bacillus Calmette-Guérin (BCG) and interleukin-2 (IL-2) . We utilized a mathematical approach for bladder cancer treatment model for derivation of ultimate upper and lower bounds and proving dissipativity property in the sense of Levinson...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
Danilo T Perez-Rivera, Veronica L Torres-Torres, Abraham E Torres-Colon, Maytee Cruz-Aponte
Diabetes mellitus is a disease characterized by a range of metabolic complications involving an individual's blood glucose levels, and its main regulator, insulin. These complications can vary largely from person to person depending on their current biophysical state. Biomedical research day-by-day makes strides to impact the lives of patients of a variety of diseases, including diabetes. One large stride that is being made is the generation of techniques to assist physicians to ``personalize medicine''. From available physiological data, biological understanding of the system, and dimensional analysis, a differential equation-based mathematical model was built in a sequential matter, to be able to elucidate clearly how each parameter correlates to the patient's current physiological state...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
Manuel Gonzalez-Navarrete
We study an alternative approach to model the dynamical behaviors of biological feedback loop, that is, a type-dependent spin system, this class of stochastic models was introduced by Fernández et. al [13], and are useful since take account to inherent variability of gene expression. We analyze a non-symmetric feedback module being an extension for the repressilator, the first synthetic biological oscillator, invented by Elowitz and Leibler [7]. We consider a mean-field dynamics for a type-dependent Ising model, and then study the empirical-magnetization vector representing concentration of molecules...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
Cameron Browne
This paper concerns modeling the coupled within-host population dynamics of virus and CTL (Cytotoxic T Lymphocyte) immune response. There is substantial evidence that the CTL immune response plays a crucial role in controlling HIV in infected patients. Recent experimental studies have demonstrated that certain CTL variants can recognize HIV infected cells early in the infected cell lifecycle before viral production, while other CTLs only detect viral proteins (epitopes) presented on the surface of infected cells after viral production...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
Shouying Huang, Jifa Jiang
In this paper, we develop and analyze an SIS epidemic model with a general nonlinear incidence rate, as well as degree-dependent birth and natural death, on heterogeneous networks. We analytically derive the epidemic threshold R0 which completely governs the disease dynamics: when R0 < 1, the disease-free equilibrium is globally asymptotically stable, i.e., the disease will die out; when R0 > 1, the disease is permanent. It is interesting that the threshold value R0 bears no relation to the functional form of the nonlinear incidence rate and degree-dependent birth...
August 1, 2016: Mathematical Biosciences and Engineering: MBE
Han Yang, Amir Sheikhi, Theo G M van de Ven
A novel biopolymer-based aerogel was developed by freeze-drying a hydrogel, synthesized from crosslinking bifunctional hairy nanocrystalline cellulose and carboxymethylated chitosan through a Schiff base reaction. The nanocelluloses, bearing aldehyde and carboxylic acid groups, facilitated the crosslinking with chitosan through imine bond formation while providing negatively-charged functional groups, and chitosan was modified to accommodate carboxylic acid. The potential of this bio-aerogel in environmental remediation was examined in a model system comprising methylene blue, a cationic dye...
October 24, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Wojciech Pulawski, Michal Jamroz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane...
October 24, 2016: Journal of Chemical Information and Modeling
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