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https://www.readbyqxmd.com/read/29167600/allergenic-asteraceae-in-air-particulate-matter-quantitative-dna-analysis-of-mugwort-and-ragweed
#1
I Müller-Germann, D A Pickersgill, H Paulsen, B Alberternst, U Pöschl, J Fröhlich-Nowoisky, V R Després
Mugwort (Artemisia vulgaris) and ragweed (Ambrosia artemisiifolia) are highly allergenic Asteraceae. They often cause pollen allergies in late summer and fall. While mugwort is native to Europe, ragweed reached Europe as a neophyte from North America about 150 years ago and continued spreading ever since. To understand possible relationships between the spread of ragweed, its abundance in air, and to judge possible health risks for the public, we quantified ragweed DNA in inhalable fine as well as in coarse air particulate matter...
2017: Aerobiologia
https://www.readbyqxmd.com/read/29166558/understanding-the-cellular-uptake-of-ph-responsive-zwitterionic-gold-nanoparticles-a-computer-simulation-study
#2
Xuebo Quan, Daohui Zhao, Libo Li, Jian Zhou
Surface functionalization of nanoparticles (NPs) with stealth polymers (e.g., hydrophilic and zwitterionic polymers) has become a common strategy to resist non-specific protein adsorption recently. Understanding the role of surface decoration on NP-biomembrane interactions is of great significance to promote the application of NPs in biomedical fields. Herein, using coarse-grained molecular dynamics (CGMD) simulations, we investigate the interactions between stealth polymer-coated gold nanoparticles (AuNPs) and lipid membranes...
November 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29166113/statistical-mechanics-of-transport-processes-in-active-fluids-equations-of-hydrodynamics
#3
Katherine Klymko, Dibyendu Mandal, Kranthi K Mandadapu
The equations of hydrodynamics including mass, linear momentum, angular momentum, and energy are derived by coarse-graining the microscopic equations of motion for systems consisting of rotary dumbbells driven by internal torques. In deriving the balance of linear momentum, we find that the symmetry of the stress tensor is broken due to the presence of non-zero torques on individual particles. The broken symmetry of the stress tensor induces internal spin in the fluid and leads us to consider the balance of internal angular momentum in addition to the usual moment of momentum...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166055/the-entropy-of-a-complex-molecule
#4
Gérôme Faure, Rafael Delgado-Buscalioni, Pep Español
Entropy is a central concept in the theory of coarse-graining. Through Einstein's formula, it provides the equilibrium probability distribution of the coarse-grained variables used to describe the system of interest. We study with molecular dynamics simulations the equilibrium probability distribution of thermal blobs representing at a coarse-grained level star polymer molecules in melt. Thermal blobs are characterized by the positions and momenta of the centers of mass, and internal energies of the molecules...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166053/towards-the-irving-kirkwood-limit-of-the-mechanical-stress-tensor
#5
E R Smith, D M Heyes, D Dini
The probability density functions (PDFs) of the local measure of pressure as a function of the sampling volume are computed for a model Lennard-Jones (LJ) fluid using the Method of Planes (MOP) and Volume Averaging (VA) techniques. This builds on the study of Heyes, Dini, and Smith [J. Chem. Phys. 145, 104504 (2016)] which only considered the VA method for larger subvolumes. The focus here is typically on much smaller subvolumes than considered previously, which tend to the Irving-Kirkwood limit where the pressure tensor is defined at a point...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166022/dynamics-of-ompf-trimer-formation-in-the-bacterial-outer-membrane-of-escherichia-coli
#6
Huilin Ma, Aliza Khan, Shikha Nangia
The self-assembly of outer membrane protein F (OmpF) in the outer membrane of Escherichia coli Gram-negative bacteria was studied using multiscale molecular dynamics simulations. To facilitate the long timescale required for protein assembly, coarse-grained parameterization of E. coli outer membrane lipids was first developed. The OmpF monomers formed stable dimers at specific protein-protein interactions sites irrespective of the lipid membrane environment. The dimer intermediate was asymmetric but provided a template to form a symmetric trimer...
November 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29161026/conditional-reversible-work-coarse-grained-models-of-molecular-liquids-with-coulomb-electrostatics-a-proof-of-concept-study-on-weakly-polar-organic-molecules
#7
Gregor Deichmann, Nico F A van der Vegt
Scale bridging simulations of soft matter rely on the availability of transferable coarse-grained models. In systematic coarse-graining approaches, core principles of statistical mechanics are used to relate the coarse-grained models to the underlying molecular interactions. The conditional reversible work (CRW) method provides effective, nonbonded pair potentials by means of computing coupling free energies between mapped chemical groups. This method has so far been used almost exclusively for systems composed of apolar organic molecules, but additional challenges arise when developing coarse-grained models for polar molecules in which (long-ranged) electrostatic interactions are important...
November 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29159013/computational-and-theoretical-approaches-for-studies-of-a-lipid-recognition-protein-on-biological-membranes
#8
REVIEW
Eiji Yamamoto
Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/29156881/mesoscale-graphene-like-honeycomb-mono-and-multi-layers-constructed-via-self-assembly-of-co-clusters
#9
Xue-Sen Hou, Guo-Long Zhu, Li-Jun Ren, Zihan Huang, Rui-Bin Zhang, Goran Ungar, Li-Tang Yan, Wei Wang
Honeycomb structure endows graphene with extraordinary properties. But could a honeycomb monolayer superlattice also be gen-erated via self-assembly of colloids or nanoparticles? Here we report the construction of mono- and multilayer molecular films with honeycomb structure that can be regarded as self-assembled artificial graphene (SAAG). We construct fan-shaped molecular building blocks by covalently connecting two kinds of clusters, one polyoxometalate (POM) and four polyhedral oligomeric silsesquioxanes (POSS)...
November 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29156125/validating-coarse-grained-voltage-activation-model-by-comparing-the-performance-to-the-results-of-mc-simulations
#10
Myungjin Lee, Vesselin Kolev, Arieh Warshel
Simulating the nature of voltage activated systems is a problem of major current interest, covering the action of voltage gated ion channels to energy storage batteries. However, fully microscopic converging molecular simulations of external voltage effects present a major challenge and macroscopic models are associated with major uncertainties about the dielectric treatment and the underlying physical basis. Recently we developed a coarse grained (CG) model that represents explicit the electrodes, the electrolytes and the membrane / protein system...
November 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29156084/role-of-charge-and-hydrophobicity-in-liprotide-formation-a-molecular-dynamics-study-with-experimental-constraints
#11
Jannik Nedergaard Pedersen, Pim Wilhelmus Johannes Maria Frederix, Jan Skov Pedersen, Siewert Jan Marrink, Daniel Otzen
Bovine α-lactalbumin (aLA) and oleate (OA) form a complex that has been intensively studied for its tumoricidal activity. Small-angle X-ray scattering (SAXS) has revealed a lipid core surrounded by partially unfolded protein. We call this type of complex a liprotide. Little is known of the molecular interactions between OA and aLA and no technique has so far provided any high resolution structure of liprotides. Here, we used coarse grained (CG) molecular dynamics (MD) simulations, Isothermal titration calorimetry (ITC) and SAXS to investigate the interactions between aLA and OA during the process of liprotide formation...
November 20, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29154885/consumers-health-related-perceptions-of-bread-implications-for-labeling-and-health-communication
#12
Pernilla Sandvik, Margaretha Nydahl, Iwona Kihlberg, Ingela Marklinder
There is a wide variety of commercial bread types and the present study identifies potential pitfalls in consumer evaluations of bread from a health perspective. The aim is to describe consumers' health-related perceptions of bread by exploring which health-related quality attributes consumers associate with bread and whether there are differences with regard to age, gender and education level. A postal and web-based sequential mixed-mode survey (n = 1134, 63% responded online and 37% by paper) with open-ended questions and an elicitation task with pictures of commercial breads were used...
November 14, 2017: Appetite
https://www.readbyqxmd.com/read/29149090/computational-methods-for-modeling-aptamers-and-designing-riboswitches
#13
REVIEW
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
https://www.readbyqxmd.com/read/29148557/structural-and-thermodynamical-properties-of-early-human-amylin-oligomers-using-replica-exchange-molecular-dynamics-mutation-effect-of-three-key-residues-f15-h18-and-f23
#14
S Bouzakraoui, N Mousseau
Human islet amyloid polypeptide (hIAPP) is a 37-residue polypeptide, considered to be the main component of the pancreatic islet amyloid associated with type 2 diabetes and is one of the most amyloidogenic polypeptides known. Although the structure of hIAPP fibrils has already been obtained, structures of early oligomers and the mechanism of β-sheet formation remain poorly understood. Herein, we characterize the atomic structure and the thermodynamics of the 14-37 residue fragment of hIAPP wild-type and mutated dimers and trimers...
November 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29148143/leaf-cell-membrane-stability-based-mechanisms-of-zinc-nutrient-in-mitigation-of-salinity-stress-in-rice
#15
Abdullah Tufail, Hong Li, Asif Naeem, Tingxian Li
Excess salts affect about 955 million ha of total arable lands worldwide and 49% of agricultural lands are Zn deficient. Soil salinity and zinc deficiency can intensify plant abiotic stress. The mechanisms by which Zn nutrients can mitigate salinity effects on plant functions are not well understood. We conducted an experiment to determine the zinc and salinity effects on rice plant retention of Zn, macronutrient potassium (K) and salt ion Na, chlorophyll formation, leaf cell membrane stability and grain yield, and to examine the mechanisms of zinc nutrition in mitigating salinity stress on plant physiological and nutritional aspects...
November 16, 2017: Plant Biology
https://www.readbyqxmd.com/read/29146934/a-continuous-13-3-ka-record-of-seismogenic-dust-events-in-lacustrine-sediments-in-the-eastern-tibetan-plateau
#16
Hanchao Jiang, Ning Zhong, Yanhao Li, Xiaolin Ma, Hongyan Xu, Wei Shi, Siqi Zhang, Gaozhong Nie
Lacustrine sediments on the eastern Tibetan Plateau (TP) contain a wealth of information on local and regional tectonic activity. High-resolution grain-size and magnetic susceptibility measurements were conducted on the 23.4-m-thick Lixian lacustrine sedimentary sequence spanning from 19.3 to 6.0 ka, revealing 70 prehistoric seismic events on the eastern TP. The seismic events caused intermittent increases in source materials that endowed the samples of an individual event layer with a gradual fining trend along the C = M line on a C (one percentile)-M (median diameter) plot...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29144758/on-the-density-dependence-of-the-integral-equation-coarse-graining-effective-potential
#17
Mohammadhasan Dinpajooh, Marina Giuseppina Guenza
Coarse-graining (CG) procedures provide computationally efficient methods for investigating the corresponding long time- and length-scale processes. In the bottom-up approaches, the effective interactions between the CG sites is obtained using the information from the atomistic simulations, but reliable CG procedures are required to preserve the structure and thermodynamics. In this regard, the integral equation coarse-graining (IECG) method is a promising approach that uses the first-principles Ornstein-Zernike equation in liquid state theory to determine the effective potential between CG sites...
November 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29144139/a-multiscale-simulation-platform-linking-lithium-ion-battery-electrode-fabrication-process-with-performance-at-the-cell-level
#18
Alain Ngandjong, Alexis Rucci, Mariem Maiza, Garima Shukla, Jorge Gabriel Vazquez-Arenas, Alejandro A Franco
A novel multiscale modeling platform is proposed to demonstrate the importance of particle assembly during battery electrode fabrication by showing its effect on battery performance. For the first time, a discretized 3D electrode resulting from the simulation of its fabrication, has been incorporated within a 3D continuum performance model. The study used LiNiMnCoO2 as active material where effect of change of electrode formulation is explored for three cases, namely 85:15, 90:10, and 95:5, as ratios between active material and carbon-binder domains...
November 16, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29142224/health-and-disease-phenotyping-in-old-age-using-a-cluster-network-analysis
#19
Jesus Felix Valenzuela, Christopher Monterola, Victor Joo Chuan Tong, Tze Pin Ng, Anis Larbi
Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142214/plastic-deformation-mechanisms-in-a-severely-deformed-fe-ni-al-c-alloy-with-superior-tensile-properties
#20
Yan Ma, Muxin Yang, Ping Jiang, Fuping Yuan, Xiaolei Wu
Nanostructured metals have high strength while they usually exhibit limited uniform elongation. While, a yield strength of approximately 2.1 GPa and a uniform elongation of about 26% were achieved in a severely deformed Fe-24.8%Ni-6.0%Al-0.38%C alloy in the present work. The plastic deformation mechanisms for the coarse-grained (CG) sample and the cold-rolled (CR) samples of this alloy were investigated by a series of mechanical tests and microstructure characterizations before and after tensile tests. No obvious phase transformation was observed during the tensile deformation for the CG sample, and the plastic deformation was found to be mainly accommodated by deformation twins and dislocation behaviors...
November 15, 2017: Scientific Reports
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