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Modeling and Simulation

Miao Liu, Ling Zhou, Baiyu Zhang, Minhong He, Xiaoying Dong, Xiaojun Lin, Chunhong Jia, Xiaochun Bai, Yifan Dai, Yongchun Su, Zhipeng Zou, Hang Zheng
Although epidemiological and preclinical studies have shown the preventative effect of n-3 polyunsaturated fatty acids (PUFAs) on colorectal cancer (CRC), the underlying molecular mechanisms are not clear. In this study, we revealed that elevation of n-3/n-6 PUFAs ratio suppress the mechanistic target of rapamycin complex 1 (mTORC1) and prevent colorectal tumorigenesis. The transgenic expression of fat-1, a desaturase that catalyzes the conversion of n-6 to n-3 PUFAs and produces n-3 PUFAs endogenously, repressed colorectal tumor cell growth and remarkably reduced tumor burden, and alleviated anemia as well as hyperlipidemia in APCMin/+ (adenomatous polyposis coli) mice, a classic CRC model that best simulates most clinical cases...
October 19, 2016: Oncotarget
Ryota Saito, Maiko Hoshi, Akihiro Kato, Chikako Ishikawa, Toshiya Komatsu
A number of (Z)-4-arylmethylene-1H-imidazol-5(4H)-ones, which are related to the fluorescent chromophore of the Aequorea green fluorescent protein (GFP), have been synthesized and evaluated their in vitro inhibitory activity against recombinant human aldose reductase for the first time. The GFP chromophore model 1a, with a p-hydroxy group on the 4-benzylidene and a carboxymethyl group on the N1 position, exhibited strong bioactivity with an IC50 value of 0.36 μM. This efficacy is higher than that of sorbinil, a known highly potent aldose reductase inhibitor...
October 8, 2016: European Journal of Medicinal Chemistry
Richard A Manderville, Stacey D Wetmore
The formation of DNA adducts by the attack of intermediates derived from toxic substances at the C8 position of 2-deoxyguanosine (dG) is a common damaging event. Although the majority of studies on C8-dG adducts have focused on lesions containing a C8-N-C tether between the bulky moiety and the nucleobase, the formation of O-linked lesions with a similar tether topology and C-linked adducts involving direct C8-C connectivity have also been uncovered. Several studies have been done to try to better understand the structural impact and mutagenicity of O-linked and C-linked aryl C8-dG adducts, including lesions arising from unsubstituted and chloro substituted phenols, and the food mutagen ochratoxin A (OTA)...
October 21, 2016: Chemical Research in Toxicology
Luisanna Cocco, Michele Marchesi
In January 3, 2009, Satoshi Nakamoto gave rise to the "Bitcoin Blockchain", creating the first block of the chain hashing on his computer's central processing unit (CPU). Since then, the hash calculations to mine Bitcoin have been getting more and more complex, and consequently the mining hardware evolved to adapt to this increasing difficulty. Three generations of mining hardware have followed the CPU's generation. They are GPU's, FPGA's and ASIC's generations. This work presents an agent-based artificial market model of the Bitcoin mining process and of the Bitcoin transactions...
2016: PloS One
Subhasree Pradhan
Spinless, interacting electrons on a finite size triangular lattice moving in an extremely strong perpendicular magnetic field are studied in comparison to a square lattice. Using a Falicov-Kimball model, the effects of Coulomb correlation, magnetic field and finite system size on their energy spectrum are observed. Exact diagonalization and Monte Carlo simulation methods (based on a modified Metropolis algorithm) have been employed to examine the recursive structure of the Hofstadter spectrum in the presence of several electronic correlation strengths for different system sizes...
October 21, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Stefan Kramel, Greg A Voth, Saskia Tympel, Federico Toschi
We introduce a new particle shape which shows preferential rotation in three dimensional homogeneous isotropic turbulence. We call these particles chiral dipoles because they consist of a rod with two helices of opposite handedness, one at each end. 3D printing is used to fabricate these particles with a length in the inertial range and their rotations are tracked in a turbulent flow between oscillating grids. High aspect ratio chiral dipoles preferentially align with their long axis along the extensional eigenvectors of the strain rate tensor, and the helical ends respond to the extensional strain rate with a mean spinning rate that is nonzero...
October 7, 2016: Physical Review Letters
Purva P Bhojane, Michael R Duff, Khushboo Bafna, Gabriella P Rimmer, Pratul K Agarwal, Elizabeth E Howell
Folate, or vitamin B9, is an important compound in one carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium towards the free ligand and protein species. This study uses vapor pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value)...
October 21, 2016: Biochemistry
Kyle D Custard, Kerri A Pratt, Siyuan Wang, Paul B Shepson
During springtime, unique halogen chemistry involving chlorine and bromine atoms controls the prevalence of volatile organic compounds, ozone, and mercury in the Arctic lower troposphere. In situ measurements of the chlorine monoxide radical (ClO) and its precursor Cl2, along with BrO and Br2, were conducted using chemical ionization mass spectrometry (CIMS) during the BRomine, Ozone, and Mercury EXperiment (BROMEX) near Barrow, Alaska in March 2012. To our knowledge, these data represent the first ClO measurements made using CIMS...
October 21, 2016: Environmental Science & Technology
Kimberly D Neely, Kate Bunton, Brad H Story
Purpose: This study used a computational vocal tract model to investigate the relationship of diphthong duration and vocal tract movement magnitude to measures of the F2 trajectory in CV words. Method: Three words (bough, boy, and buy) were simulated on the basis of an adult female vocal tract model, in which the model parameters were estimated from audio recordings of a female talker. Model parameters were then modified to generate 35 simulations of each word corresponding to 7 different durations and 5 movement magnitude settings...
October 20, 2016: Journal of Speech, Language, and Hearing Research: JSLHR
Michael P Grubb, Philip M Coulter, Hugo J B Marroux, Balazs Hornung, Ryan S McMullen, Andrew J Orr-Ewing, Michael N R Ashfold
Spectroscopically observing the translational and rotational motion of solute molecules in liquid solutions is typically impeded by their interactions with the solvent, which conceal spectral detail through linewidth broadening. Here we show that unique insights into solute dynamics can be made with perfluorinated solvents, which interact weakly with solutes and provide a simplified liquid environment that helps to bridge the gap in our understanding of gas- and liquid-phase dynamics. Specifically, we show that in such solvents, the translational and rotational cooling of an energetic CN radical can be observed directly using ultrafast transient absorption spectroscopy...
November 2016: Nature Chemistry
Mon-Shu Ho, Chih-Pong Huang, Jyun-Hwei Tsai, Che-Fu Chou, Wen-Jay Lee
This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors...
September 28, 2016: Journal of Visualized Experiments: JoVE
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
Baohua Yue, Ron Brendel, Amelia Lukitsch, Thomas Prentice, Brian Doty
BACKGROUND: Commercial baclofen formulations used with infusion pumps are available at therapeutic concentrations of 0.5-2.0 mg/mL. However, patients who receive higher daily doses of baclofen may benefit from products with greater baclofen concentrations since their refill frequency would be reduced (up to a maximum of 180 days). We evaluated baclofen solubility, baclofen 3 mg/mL intrathecal (IT) formulation stability, and chemical and physical compatibility with Medtronic SynchroMed(®) II and Codman Medstream(®) programmable IT infusion pumps...
October 21, 2016: Neuromodulation: Journal of the International Neuromodulation Society
Dominic Woolf, Johannes Lehmann, David R Lee
Restricting global warming below 2 °C to avoid catastrophic climate change will require atmospheric carbon dioxide removal (CDR). Current integrated assessment models (IAMs) and Intergovernmental Panel on Climate Change scenarios assume that CDR within the energy sector would be delivered using bioenergy with carbon capture and storage (BECCS). Although bioenergy-biochar systems (BEBCS) can also deliver CDR, they are not included in any IPCC scenario. Here we show that despite BECCS offering twice the carbon sequestration and bioenergy per unit biomass, BEBCS may allow earlier deployment of CDR at lower carbon prices when long-term improvements in soil fertility offset biochar production costs...
October 21, 2016: Nature Communications
Martin Leder, Christopher Grossert, Lukas Sitta, Maximilian Genske, Achim Rosch, Martin Weitz
To describe a mobile defect in polyacetylene chains, Su, Schrieffer and Heeger formulated a model assuming two degenerate energy configurations that are characterized by two different topological phases. An immediate consequence was the emergence of a soliton-type edge state located at the boundary between two regions of different configurations. Besides giving first insights in the electrical properties of polyacetylene materials, interest in this effect also stems from its close connection to states with fractional charge from relativistic field theory...
October 21, 2016: Nature Communications
Dureid Qazzazie, Mohammad Halhouli, Olena Yurchenko, Gerald Urban
The lack of performance of graphene-based electrocatalysts for oxygen reduction (ORR) is a major concern for fuel cells which can be mastered using nanocomposites. This work is highlighted by the optimization of nitrogen(N)-doped graphene/carbon nanotubes (CNTs) nanocomposite's ORR performance examined by galvanostatic measurements in realistically approached glucose half-cells. Obtained results mark an essential step for the development of nanocarbon-based cathodes, as we specifically evaluate the electrode performance under real fuel cell conditions...
October 21, 2016: Nanotechnology
Shaher Bano Mirza, Ramin Ekhteiari Salmas, M Qaiser Fatmi, Serdar Durdagi
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a)...
October 21, 2016: Journal of Enzyme Inhibition and Medicinal Chemistry
Astha Garg, Charles A Cartier, Kyle J M Bishop, Darrell Velegol
The zeta potential of a particle characterizes its motion in an electric field and is often thought to be negligible at high ionic strength (several moles per liter) due to thinning of the electrical double layer (EDL). Here, we describe zeta potential measurements on polystyrene latex (PSL) particles at monovalent salt concentrations up to saturation (~ 5 M NaCl) using electrophoresis in sinusoidal electric fields and high-speed video microscopy. Our measurements reveal that the zeta potential remains finite at even the highest concentrations...
October 21, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Zhimin Xie, Dongliang Chai, Youshan Wang, Huifeng Tan
The effective potentials are of great importance for the coarse-grained (CG) simulations, which can be obtained by the structure-based iterative Boltzmann inversion (IBI) method. However, the standard IBI method is incapable of keeping the mechanical and thermodynamic properties of the CG model in consistence with those of the all-atom model. Unlike the existed techniques, such as introducing the friction force as the dissipative force to drop the superatom motion while the conservative force arising from the CG potential was kept intact, we directly modified the standard IBI nonbonded potential by adding an empirical function...
October 21, 2016: Journal of Physical Chemistry. B
Erfan Dashtimoghadam, Ghasem Bahlakeh, Hamed Salimi-Kenari, Mohammad Mahdi Hasani-Sadrabadi, Hamid Mirzadeh, Bo Nyström
The temperature-induced gelation of chitosan/glycerophosphate (Chs/GP) systems through physical interactions has shown great potential for various biomedical applications. In the present work, hydroxyethyl cellulose (HEC) was added to the thermosensitive Chs/GP solution to improve the mechanical strength and gel properties of the incipient Chs/HEC/GP gel in comparison with the Chs/GP hydrogel at body temperature. The physical features of the macromolecular complexes formed by the synergistic interaction between chitosan and hydroxyethyl cellulose in the presence of β-glycerophosphate disodium salt solution have been studied essentially from a rheological point of view...
October 21, 2016: Biomacromolecules
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