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Computational model

Stephanie A Parker, Linus Amarikwa, Kevin Vehar, Raquel Orozco, Scott Godfrey, Jon Coffman, Parviz Shamlou, Cameron L Bardliving
Insufficient mixing in laminar flow reactors due to diffusion-dominated flow limits their use in applications where narrow residence time distribution (RTD) is required. The aim of this study was to design and characterize a laminar flow (Re 187.7-375.5) tubular reactor for low pH viral inactivation with enhanced radial mixing via the incorporation of curvature and flow inversions. Towards this aim, the reactor described here, Jig in a Box (JIB), was designed with a flow path consisting of alternating 270° degree turns...
November 18, 2017: Biotechnology and Bioengineering
Jourdan Colter, Barbara Wirostko, Brittany Coats
Drug-loaded hydrogel devices are emerging as an effective means of localized and sustained drug delivery for the treatment of corneal conditions and injuries. One such device uses a novel, thiolated crosslinked carboxymethylated, hyaluronic acid-based hydrogel (CMHA-S) film to deliver drug to the ocular surface upon placement into the inferior fornix of the eye. While proven to be very safe and effective, the CMHA-S film tends to dislodge in the highly-lubricated ocular environment, thereby reducing drug delivery efficiency and drug efficacy...
November 17, 2017: Annals of Biomedical Engineering
Jun Young Park, Chong Wu, Saonli Basu, Matt McGue, Wei Pan
In genome-wide association studies (GWAS), it has been increasingly recognized that, as a complementary approach to standard single SNP analyses, it may be beneficial to analyze a group of functionally related SNPs together. Among the existent population-based SNP-set association tests, two adaptive tests, the aSPU test and the aSPUpath test, offer a powerful and general approach at the gene- and pathway-levels by data-adaptively combining the results across multiple SNPs (and genes) such that high statistical power can be maintained across a wide range of scenarios...
November 17, 2017: Behavior Genetics
Ying Tang, Ruoshi Yuan, Gaowei Wang, Xiaomei Zhu, Ping Ao
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including the cell-fate decision in developmental processes as well as the genesis and progression of cancers. While various attempts have been made to construct potential landscape in high dimensional systems and to estimate transition rates, they are practically limited to the cases where either noise is small or detailed balance condition holds. A general and practical approach to investigate real-world nonequilibrium systems, which are typically high-dimensional and subject to large multiplicative noise and the breakdown of detailed balance, remains elusive...
November 17, 2017: Scientific Reports
Jaechang Lim, Sungwoo Kang, Jaewook Kim, Woo Youn Kim, Seol Ryu
Plasmonic nanoparticles in the quantum regime exhibit characteristic optical properties that cannot be described by classical theories. Time-dependent density functional theory (TDDFT) is rising as a versatile tool for study on such systems, but its application has been limited to very small clusters due to rapidly growing computational costs. We propose an atomistic dipole-interaction-model for quantum plasmon simulations as a practical alternative. Namely the atomic dipole approximation represents induced dipoles with atomic polarizabilities obtained from TDDFT without empirical parameters...
November 17, 2017: Scientific Reports
C Le Fèvre, L Poty, G Noël
The many advances in data collection computing systems (data collection, database, storage), diagnostic and therapeutic possibilities are responsible for an increase and a diversification of available data. Big data offers the capacities, in the field of health, to accelerate the discoveries and to optimize the management of patients by combining a large volume of data and the creation of therapeutic models. In radiotherapy, the development of big data is attractive because data are very numerous et heterogeneous (demographics, radiomics, genomics, radiogenomics, etc...
November 14, 2017: Cancer Radiothérapie: Journal de la Société Française de Radiothérapie Oncologique
Peter Bossaerts, Carsten Murawski
The rationality principle postulates that decision-makers always choose the best action available to them. It underlies most modern theories of decision-making. The principle does not take into account the difficulty of finding the best option. Here, we propose that computational complexity theory (CCT) provides a framework for defining and quantifying the difficulty of decisions. We review evidence showing that human decision-making is affected by computational complexity. Building on this evidence, we argue that most models of decision-making, and metacognition, are intractable from a computational perspective...
December 2017: Trends in Cognitive Sciences
Mohammad Hadi Hafezi, Tribikram Kundu
The interaction between surface wave and a surface breaking crack is studied using a novel fast modeling tool called peri-ultrasound that can model both linear and nonlinear ultrasonic response. This modeling approach is based on peridynamic theory. In this study, the surface wave is modeled by applying a triangular pulse excitation function on the surface of a large structure. The particle movements are simulated on both sides of the surface crack to investigate transmitted and reflected fields. This investigation shows that: (1) the computed amplitude spectra of the Rayleigh wave agrees with the experimental observation; and (2) the structure containing a surface breaking crack shows noticeable increase in its nonlinear behavior...
November 7, 2017: Ultrasonics
Zhengwang Wu, Yanrong Guo, Sang Hyun Park, Yaozong Gao, Pei Dong, Seong-Whan Lee, Dinggang Shen
We propose a robust and efficient learning-based deformable model for segmenting regions of interest (ROIs) from structural MR brain images. Different from the conventional deformable-model-based methods that deform a shape model locally around the initialization location, we learn an image-based regressor to guide the deformable model to fit for the target ROI. Specifically, given any voxel in a new image, the image-based regressor can predict the displacement vector from this voxel towards the boundary of target ROI, which can be used to guide the deformable segmentation...
November 10, 2017: Medical Image Analysis
Zhiye Tang, Chia-En A Chang
Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-timescale molecular dynamics (MD) simulations, post-analysis and numerical calculations...
November 17, 2017: Journal of Chemical Theory and Computation
Zhuoqin Yu, Pengfei Li, Kenneth M Merz
An empirical approach based on the previously developed zinc AMBER force field (ZAFF) is proposed for the determination of the parameters for bonds and angles involving zinc. We call it the extended ZAFF (EZAFF) model because the original ZAFF model was only formulated for 4-coordinated systems, while EZAFF additionally can tackle 5- and 6-coordinated systems. Tests were carried out for 6 metalloproteins and 5 organometallic compounds with different coordination spheres. Results validated the reliability of the current model to handle a variety of zinc containing complexes...
November 17, 2017: Journal of Chemical Theory and Computation
Mohamad Mohebifar, Erin R Johnson, Christopher N Rowley
London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential, using empirically-determined parameters. These parameters are generally underdetermined and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields...
November 17, 2017: Journal of Chemical Theory and Computation
Wenyi Wang, Alexander Sedykh, Hainan Sun, Linlin Zhao, Daniel P Russo, Hongyu Zhou, Bing Yan, Hao Zhu
The discovery of biocompatible or bioactive nanoparticles for medicinal applications is an expensive and time-consuming process that may be significantly facilitated by incorporating more rational approaches combining both experimental and computational methods. However, it is currently hindered by two limitations: 1) the lack of high quality comprehensive data for computational modeling, and 2) the lack of an effective modeling method for the complex nanomaterial structures. In this study, we tackled both issues by first synthesizing a large library of nanoparticles and obtained comprehensive data on their characterizations and bioactivities...
November 17, 2017: ACS Nano
T Morlat, A C Fernandes, M Felizardo, A Kling, T A Girard, J G Marques, F P Carvalho
Superheated droplet detectors (SDDs) are traditionally employed in the detection of neutrons. In this work the focus is on the detection of alpha particles using C2ClF5 as the target liquid. The alpha-droplet interaction is examined via computational studies, and a geometric model developed to describe the expected detector response. Experiments with alpha-emitting uranium- and samarium-doped SDDs at temperatures of 5-12°C confirm that the event rate is related to the size of the droplets, and are in model agreement for temperatures below 8°C; above this temperature, the acoustic sensitivity is reduced by signal attenuation as a result of the increasing bubble population, for which the addition of an attenuation coefficient restores the agreement with experiment...
November 15, 2017: Radiation Protection Dosimetry
Matthew Z DeMaere, Aaron E Darling
Background: Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings: We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences...
November 15, 2017: GigaScience
Guillaume Saulière, Jérôme Dedecker, Laurie-Anne Marquet, Pierre Rochcongar, Jean-Francois Toussaint, Geoffroy Berthelot
The clinical and biological follow-up of individuals, such as the biological passport for athletes, is typically based on the individual and longitudinal monitoring of hematological or urine markers. These follow-ups aim to identify abnormal behavior by comparing the individual's biological samples to an established baseline. These comparisons may be done via different ways, but each of them requires an appropriate extra population to compute the significance levels, which is a non-trivial issue. Moreover, it is not necessarily relevant to compare the measures of a biomarker of a professional athlete to that of a reference population (even restricted to other athletes), and a reasonable alternative is to detect the abnormal values by considering only the other measurements of the same athlete...
November 15, 2017: Biostatistics
Tzu-Hsiang Lin, Hsin-Tai Hu, Hsueh-Chun Wang, Meng-Chian Wu, Shu-Wei Wu, Ming-Long Yeh
The success of many endosseous implants in orthopaedic and dental applications depends on the surface characteristics, as they affect osseous integration. Previous investigations indicated that a novel large-grit sand-blasted and acid-etched (SLA) titanium (denoted as SLAffinity-Ti) implant had better bone integration than that of a comparably shaped implant with a plasma-sprayed titanium surface. The purpose of the present investigation was to create a SLAffinity surface on pedicle screws and trauma screws and to compare it with the surfaces of a sand-blasted-only implant and commercial implants in terms of bone integration...
2017: PloS One
Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers...
November 17, 2017: International Journal of Molecular Sciences
Dorottya Cserpán, Domokos Meszéna, Lucia Wittner, Kinga Tóth, István Ulbert, Zoltán Somogyvári, Daniel K Wojcik
Revealing the current source distribution along the neuronal membrane is a key step on the way to understanding neural computations, however, the experimental and theoretical tools to achieve sufficient spatiotemporal resolution for the estimation remain to be established. Here we address this problem using extracellularly recorded potentials with arbitrarily distributed electrodes for a neuron of known morphology. We use simulations of models with varying complexity to validate the proposed method and to give recommendations for experimental applications...
November 17, 2017: ELife
Marta Arczewska, Daniel M Kamiński, Barbara Gieroba, Mariusz Gagoś
UV-vis spectrophotometry has been applied to determine acid dissociation constants of the prenylated chalcone xanthohumol. The pKa values were compared with those derived from pH-metric titrations. The order of the deprotonation site in the xanthohumol molecule was estimated by quantum mechanical calculations as 2'-OH, 4'-OH, and 4-OH. Furthermore, the electronic and spectroscopic properties of xanthohumol have been investigated on the basis of the time-dependent density functional theory (TDDFT). The TDDFT method, combined with a hybrid exchange-correlation functional using the B3LYP and CAM-B3LYP levels of theory in conjunction with the SMD solvation model, was used to optimize all geometries and predict the excitation energies of the neutral form and ionized species of the chalcone depending on pH value...
November 17, 2017: Journal of Natural Products
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