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https://www.readbyqxmd.com/read/28095402/a-general-shear-dependent-model-for-thrombus-formation
#1
Alireza Yazdani, He Li, Jay D Humphrey, George Em Karniadakis
Modeling the transport, activation, and adhesion of platelets is crucial in predicting thrombus formation and growth following a thrombotic event in normal or pathological conditions. We propose a shear-dependent platelet adhesive model based on the Morse potential that is calibrated by existing in vivo and in vitro experimental data and can be used over a wide range of flow shear rates ([Formula: see text]). We introduce an Eulerian-Lagrangian model where hemodynamics is solved on a fixed Eulerian grid, while platelets are tracked using a Lagrangian framework...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28094239/performance-variation-due-to-stiffness-in-a-tuna-inspired-flexible-foil-model
#2
Mariel-Luisa N Rosic, Patrick J M Thornycroft, Kara L Feilich, Kelsey N Lucas, George V Lauder
Tuna are fast, economical swimmers in part due to their stiff, high aspect ratio caudal fins and streamlined bodies. Previous studies using passive caudal fin models have suggested that while high aspect ratio tail shapes such as a tuna's generally perform well, tail performance cannot be determined from shape alone. In this study, we analyzed the swimming performance of tuna-tail-shaped hydrofoils of a wide range of stiffnesses, heave amplitudes, and frequencies to determine how stiffness and kinematics affect multiple swimming performance parameters for a single foil shape...
January 17, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28092501/parallel-molecular-distributed-detection-with-brownian-motion
#3
Uri Rogers, Min-Sung Koh
This paper explores the in vivo distributed detection of an undesired biological agent's (BAs) biomarkers by a group of biological sized nanomachines in an aqueous medium under drift. The term distributed, indicates that the system information relative to the BAs presence is dispersed across the collection of nanomachines, where each nanomachine possesses limited communication, computation, and movement capabilities. Using Brownian motion with drift, a probabilistic detection and optimal data fusion framework, coined molecular distributed detection, will be introduced that combines theory from both molecular communication and distributed detection...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092500/a-model-of-a-synthetic-biological-communication-interface-between-mammalian-cells-and-mechatronic-systems
#4
Keith C Heyde, Warren C Ruder
The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cell-robot system, with a specific focus on the design of the synthetic gene networks needed for the system...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28089359/transient-and-long-time-kinetic-responses-of-the-cadaveric-leg-during-internal-and-external-foot-rotation
#5
Alexander R Mait, Adwait Mane, Jason L Forman, John Paul Donlon, Bingbing Nie, Richard W Kent
The purpose of this study was to determine the long-time and transient characteristics of the moment generated by external (ER) and internal (IR) rotation of the calcaneus with respect to the tibia. Two human cadaver legs were disarticulated at the knee joint while maintaining the connective tissue between the tibia and fibula. An axial rotation of 21° was applied to the proximal tibia to generate either ER or IR while the fibula was unconstrained and the calcaneus was permitted to translate in the transverse plane...
January 7, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28088482/combined-spatiotemporal-ica-stica-for-continuous-and-dynamic-lag-structure-analysis-of-mreg-data
#6
Ville Raatikainen, Niko Huotari, Vesa Korhonen, Aleksi Rasila, Janne Kananen, Lauri Raitamaa, Tuija Keinänen, Jussi Kantola, Osmo Tervonen, Vesa Kiviniemi
This study investigated lag structure in the resting-state fMRI by applying a novel independent component (ICA) method to magnetic resonance encephalography (MREG) data. Briefly, the spatial ICA (sICA) was used for defining the frontal and back nodes of the default mode network (DMN), and the temporal ICA (tICA), which is enabled by the high temporal resolution of MREG (TR=100ms), was used to separate both neuronal and physiological components of these two spatial map regions. Subsequently, lag structure was investigated between the frontal (DMNvmpf) and posterior (DMNpcc) DMN nodes using both conventional method with all-time points and a sliding-window approach...
January 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28078892/dynamical-transitions-at-low-temperatures-in-the-nearest-hydration-shell-of-phospholipid-bilayers
#7
Victoria N Syryamina, Sergei Andreevich Dzuba
For the so-called dynamical transition from harmonic to anharmonic (or diffusive) motions in biological systems, the presence of hydration water is important. To explain the molecular mechanism of this transition, the information on molecular motions in the nearest hydration shell would be helpful. In this work, to study molecular motions in the nearest hydration shell of spin-labeled model biological membranes, a pulsed version of electron paramagnetic resonance (EPR)-electron spin echo envelope modulation (ESEEM) spectroscopy-is employed...
January 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28076811/modeling-the-effect-of-curvature-on-the-collective-behavior-of-cells-growing-new-tissue
#8
Mohd Almie Alias, Pascal R Buenzli
The growth of several biological tissues is known to be controlled in part by local geometrical features, such as the curvature of the tissue interface. This control leads to changes in tissue shape that in turn can affect the tissue's evolution. Understanding the cellular basis of this control is highly significant for bioscaffold tissue engineering, the evolution of bone microarchitecture, wound healing, and tumor growth. Although previous models have proposed geometrical relationships between tissue growth and curvature, the role of cell density and cell vigor remains poorly understood...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28074936/hygroscopic-motions-of-fossil-conifer-cones
#9
Simon Poppinga, Nikolaus Nestle, Andrea Šandor, Bruno Reible, Tom Masselter, Bernd Bruchmann, Thomas Speck
Conifer cones represent natural, woody compliant structures which move their scales as passive responses to changes in environmental humidity. Here we report on water-driven opening and closing motions in coalified conifer cones from the Eemian Interglacial (approx. 126,000-113,000 years BP) and from the Middle Miocene (approx. 16.5 to 11.5 million years BP). These cones represent by far the oldest documented evidence of plant parts showing full functionality of such passive hydraulically actuated motion. The functional resilience of these structures is far beyond the biological purpose of seed dispersal and protection and is because of a low level of mineralization of the fossils...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068771/perturbation-approach-for-computing-infrared-spectra-of-the-local-mode-of-probe-molecules
#10
Rui-Jie Xue, Adam Grofe, He Yin, Zexing Qu, Jiali Gao, Hui Li
Linear and two-dimensional infrared (IR) spectroscopy of site-specific probe molecules provides an opportunity to gain a molecular-level understanding of the local hydrogen-bonding network, conformational dynamics, and long-range electrostatic interactions in condensed-phase and biological systems. A challenge in computation is to determine the time-dependent vibrational frequencies that incorporate explicitly both nuclear quantum effects of vibrational motions and an electronic structural representation of the potential energy surface...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28064020/impact-of-geometry-changes-in-the-channel-pore-by-the-gating-movements-on-the-channel-s-conductance
#11
Agata Wawrzkiewicz-Jałowiecka, Przemysław Borys, Zbigniew J Grzywna
Kv 1.2 are voltage-dependent potassium channels of great biological importance. Despite the existence of many reports considering structure - function relations of the Kv 1.2 channel's quantitative domains, some details of the voltage gating remain ambiguous, or even unknown. One of the examples is the range of the S4-S6 domains motions involved in channel activation and gating. Another important question is to what extent the channel geometry influences the observable channel conductance at different voltages, and what mechanism stands behind...
January 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28060489/watching-proteins-wiggle-mapping-structures-with-two-dimensional-infrared-spectroscopy
#12
Ayanjeet Ghosh, Joshua S Ostrander, Martin T Zanni
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics...
January 6, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28058428/incorporation-of-aspirin-modulates-the-dynamical-and-phase-behavior-of-the-phospholipid-membrane
#13
V K Sharma, E Mamontov, M Ohl, M Tyagi
Nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most widely used medications in the world for their analgesic, antipyretic, and anti-inflammatory actions, despite a well-known incidence of a wide spectrum of their adverse effects. To a great extent, beneficial action and side effects of NSAIDs are associated with the interaction of these drugs at the cell membrane level. Here, we use neutron scattering to combine elastic intensity scans, quasielastic and neutron spin echo (NSE) measurements to understand the effect of aspirin, a commonly used NSAID, on the dynamical and phase behavior of the membrane of dimyristoylphosphatidylcholine (DMPC), a prominent representative of phospholipids residing in the outer leaflet of the human erythrocyte membrane...
January 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28051858/quantum-mechanical-enhancement-of-rate-constants-and-kinetic-isotope-effects-for-water-mediated-proton-transfer-in-a-model-biological-system
#14
James W Mazzuca, Chase P Schultz
Biological systems have been shown to shuttle excess protons long distances by taking advantage of tightly organized hydrogen-bonded water bridges in hydrophobic protein cavities, and similar effects have been observed in carbon nanotubes. In this theoretical study we investigate how quantum effects of proton motion impact the rate constants for charge transfer in a model system consisting of a donor and acceptor molecule separated by a single-molecule water bridge. We calculate quantum and classical rate constants for the transfer of an excess proton over two possible paths, one with an H3O(+) intermediate, and one with an OH(-) intermediate...
January 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28047771/su-g-tep3-07-on-the-development-of-mechano-biological-assessment-of-leukemia-cells-using-optical-tweezers
#15
E Brost, J Brooks, J Piepenburg, S Chakraborty, T Das, A Green, Y Watanabe, S Hui
PURPOSE: Patients with BCR-ABL (Ph +ve) acute lymphoblastic leukemia are at very high risk of relapse and mortality. In line with the NIH mission to understand the physical and biological processes, we seek to report mechano-biological method to assessment and distinguish treated/untreated leukemia cells. METHODS: BCR-ABL leukemia cell populations and silica microspheres were trapped in a 100x magnification optical trapping system (λ=660 nm, 70 mW). Light refracted through the trapped sample was collected in the back focal plane by a quadrant detector to measure the positions of individual cells...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047696/su-d-brc-05-effects-of-motion-and-variable-rbe-in-a-lung-patient-treated-with-passively-scattered-protons
#16
D Mirkovic, U Titt, P Yepes, R Mohan
PURPOSE: To evaluate effects of motion and variable relative biological effectiveness (RBE) in a lung cancer patient treated with passively scattered proton therapy using dose volume histograms associated with patient dose computed using three different methods. METHODS: A proton treatment plan of a lung cancer patient optimized using clinical treatment planning system (TPS) was used to construct a detailed Monte Carlo (MC) model of the beam delivery system and the patient specific aperture and compensator...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046972/mo-a-201-00-a-cliff-s-notes-version-of-proton-therapy
#17
Jon Kruse
: Proton therapy is a rapidly growing modality in the fight against cancer. From a high-level perspective the process of proton therapy is identical to x-ray based external beam radiotherapy. However, this course is meant to illustrate for x-ray physicists the many differences between x-ray and proton based practices. Unlike in x-ray therapy, proton dose calculations use CT Hounsfield Units (HU) to determine proton stopping power and calculate the range of a beam in a patient. Errors in stopping power dominate the dosimetric uncertainty in the beam direction, while variations in patient position determine uncertainties orthogonal to the beam path...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046335/su-g-jep4-09-impact-of-interfractional-motion-on-hypofractionated-pencil-beam-scanning-proton-therapy-for-prostate-cancer
#18
M Moteabbed, A Trofimov, G Sharp, Y Wang, A Zietman, J Efstathiou, H Lu
PURPOSE: To investigate the impact of anatomy/setup variations on standard vs. hypofractionated anterolateral pencil beam scanning (PBS) proton therapy for prostate cancer. METHODS: Six prostate cancer patients treated with double-scattering proton therapy, who underwent weekly verification CT scans were selected. Implanted fiducials were used for localization, and endorectal balloons for immobilization. New PBS plans using combination of lateral and anterior-oblique (AO) (±35 deg) beams were created...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046311/mo-a-201-01-a-cliff-s-notes-version-of-proton-therapy
#19
J Kruse
: Proton therapy is a rapidly growing modality in the fight against cancer. From a high-level perspective the process of proton therapy is identical to x-ray based external beam radiotherapy. However, this course is meant to illustrate for x-ray physicists the many differences between x-ray and proton based practices. Unlike in x-ray therapy, proton dose calculations use CT Hounsfield Units (HU) to determine proton stopping power and calculate the range of a beam in a patient. Errors in stopping power dominate the dosimetric uncertainty in the beam direction, while variations in patient position determine uncertainties orthogonal to the beam path...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28039557/on-the-mechanical-analogue-of-dna
#20
Ludmila Yakushevich
The creation of mechanical analogues of biological systems is known as a useful instrument that helps to understand better the dynamical mechanisms of the functioning of living organisms. Mechanical analogues of biomolecules are usually constructed for imitation of their internal mobility, which is one of the most important properties of the molecules. Among the different types of internal motions, angular oscillations of nitrous bases are of special interest because they make a substantial contribution to the base pairs opening that in turn is an important element of the process of the DNA-protein recognition...
December 30, 2016: Journal of Biological Physics
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