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https://www.readbyqxmd.com/read/29906978/island-size-distribution-with-hindered-aggregation
#1
Diego Luis González, Manuel Camargo, Julián A Sánchez
We study the effect of hindered aggregation on the island formation processes for a one-dimensional model of epitaxial growth with arbitrary nucleus size i. In the proposed model, the attachment of monomers to islands is hindered by an aggregation barrier, ε_{a}, which decreases the hopping rate of monomers to the islands. As ε_{a} increases, the system exhibits a crossover between two different regimes; namely, from diffusion-limited aggregation to attachment-limited aggregation. The island size distribution, P(s), is calculated for different values of ε_{a} by a self-consistent approach involving the nucleation and aggregation capture kernels...
May 2018: Physical Review. E
https://www.readbyqxmd.com/read/29906144/hydrogen-diffusion-and-trapping-in-%C3%AE-iron-the-role-of-quantum-and-anharmonic-fluctuations
#2
Bingqing Cheng, Anthony T Paxton, Michele Ceriotti
We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect...
June 1, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29900356/data-sets-of-migration-barriers-for-atomistic-kinetic-monte-carlo-simulations-of-fe-self-diffusion
#3
Ekaterina Baibuz, Simon Vigonski, Jyri Lahtinen, Junlei Zhao, Ville Jansson, Vahur Zadin, Flyura Djurabekova
Atomistic rigid lattice Kinetic Monte Carlo (KMC) is an efficient method for simulating nano-objects and surfaces at timescales much longer than those accessible by molecular dynamics. A laborious and non-trivial part of constructing any KMC model is, however, to calculate all migration barriers that are needed to give the probabilities for any atom jump event to occur in the simulations. We calculated three data sets of migration barriers for Fe self-diffusion: barriers of first nearest neighbour jumps, second nearest neighbours hop-on jumps on the Fe {100} surface and a set of barriers of the diagonal exchange processes for various cases of the local atomic environments within the 2nn coordination shell...
August 2018: Data in Brief
https://www.readbyqxmd.com/read/29850708/intrinsic-charge-mobility-in-benzothieno-3-2-b-1-benzothiophene-btbt-organic-semiconductors-is-enhanced-with-long-alkyl-side-chains
#4
M Alkan, I Yavuz
Recent measurements show that organic materials with a conjugated benzothieno-benzothiophene (BTBT) core exhibit unprecedented charge-carrier mobilities, dramatically influenced by the size of the side-chains. Using a multitude of computational tools, we, in depth, calculate the molecular ordering and charge-transport of these materials to rationalize the side-chain dependence. The reported experimental hole mobilities typically fall within the range of 1-100 cm2 V-1 s-1, therefore we employ both band transport models using deformation-potential theory based on DFT-D3 methodology and hopping transport using kinetic Monte Carlo simulations employing Marcus-Levich-Jortner charge-transfer theory...
May 31, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29715428/kinetics-of-huperzine-a-dissociation-from-acetylcholinesterase-via-multiple-unbinding-pathways
#5
Jakub Rydzewski, Rafal Jakubowski, Wieslaw Nowak, Helmut Grubmüller
The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase (TcAChE) was investigated by 4-microsecond unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front-door along the axis of the active-site gorge (pwf) and through a new transient side-door (pws), i...
May 1, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29677468/exploring-energy-landscapes
#6
David J Wales
Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations...
April 20, 2018: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/29652509/exciton-delocalizing-ligands-can-speed-up-energy-migration-in-nanocrystal-solids
#7
Michael S Azzaro, Amro Dodin, Diana Y Zhang, Adam P Willard, Sean T Roberts
Researchers have long sought to use surface ligands to enhance energy migration in nanocrystal solids by decreasing the physical separation between nanocrystals and strengthening their electronic coupling. Exciton-delocalizing ligands, which possess frontier molecular orbitals that strongly mix with nanocrystal band-edge states, are well-suited for this role because they can facilitate carrier-wave function extension beyond the nanocrystal core, reducing barriers for energy transfer. This report details the use of the exciton-delocalizing ligand phenyldithiocarbamate (PDTC) to tune the transport rate and diffusion length of excitons in CdSe nanocrystal solids...
May 9, 2018: Nano Letters
https://www.readbyqxmd.com/read/29604823/force-feedback-effects-on-single-molecule-hopping-and-pulling-experiments
#8
M Rico-Pasto, I Pastor, F Ritort
Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model...
March 28, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29569915/molecular-facts-on-the-structure-and-dynamics-of-electrolyte-species-in-cu-cl-cycle-for-hydrogen-generation-an-insight-from-molecular-dynamic-simulations
#9
Pooja Sahu, Sk Musharaf Ali, K T Shenoy, S Mohan
The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations...
April 12, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29542770/insight-into-fast-ion-migration-kinetics-of-a-new-hybrid-single-li-ion-conductor-based-on-aluminate-complexes-for-solid-state-li-ion-batteries
#10
Yancong Feng, Rui Tan, Yan Zhao, Rongtan Gao, Luyi Yang, Jinlong Yang, Hao Li, Guofu Zhou, Haibiao Chen, Feng Pan
A novel hybrid single Li-ion conductor (SLIC) for a Li-ion solid electrolyte was prepared by mixing aluminate complexes-polyethylene glycol (LiAl-PEG) and polyethylene oxide (PEO) for solid-state Li-ion batteries. The LiAl-PEG/PEO blend possesses high thermal stability and electrochemical stability with an oxidation decomposition voltage up to 4.8 V. Notably, this hybrid SLIC exhibits not only excellent Li-ion migration kinetics, but also good ionic conductivity as high as 4.0 × 10-5 and 2.6 × 10-4 S cm-1 at 30 and 100 °C, respectively, which is much higher than previously reported SLICs...
March 29, 2018: Nanoscale
https://www.readbyqxmd.com/read/29533358/kinetic-analysis-of-horizontal-plyometric-exercise-intensity
#11
Andrew J Kossow, William P Ebben
Kossow, AJ, DeChiara, TG, Neahous, SM, and Ebben, WP. Kinetic analysis of horizontal plyometric exercise intensity. J Strength Cond Res 32(5): 1222-1229, 2018-Plyometric exercises are frequently performed as part of a strength and conditioning program. Most studies assessed the kinetics of plyometric exercises primarily performed in the vertical plane. The purpose of this study was to evaluate the multiplanar kinetic characteristics of a variety of plyometric exercises, which have a significant horizontal component...
May 2018: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/29488380/morphology-determines-conductivity-and-seebeck-coefficient-in-conjugated-polymer-blends
#12
Guangzheng Zuo, Xianjie Liu, Mats Fahlman, Martijn Kemerink
The impact of nanoscale morphology on conductivity and Seebeck coefficient in p-type doped all-polymer blend systems is investigated. For a strongly phase separated system (P3HT:PTB7), we achieve a Seebeck coefficient that peaks at S ∼ 1100 μV/K with conductivity σ ∼ 3 × 10-3 S/cm for 90% PTB7. In marked contrast, for well-mixed systems (P3HT:PTB7 with 5% diiodooctane (DIO), P3HT:PCPDTBT), we find an almost constant S ∼ 140 μV/K and σ ∼ 1 S/cm despite the energy levels being (virtually) identical in both cases...
March 21, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29483548/sculpting-nanoparticle-dynamics-for-single-bacteria-level-screening-and-direct-binding-efficiency-measurement
#13
Y Z Shi, S Xiong, Y Zhang, L K Chin, Y Chen, J B Zhang, T H Zhang, W Ser, A Larson, L S Hoi, J H Wu, T N Chen, Z C Yang, Y L Hao, B Liedberg, P H Yap, D P Tsai, C-W Qiu, A Q Liu
Particle trapping and binding in optical potential wells provide a versatile platform for various biomedical applications. However, implementation systems to study multi-particle contact interactions in an optical lattice remain rare. By configuring an optofluidic lattice, we demonstrate the precise control of particle interactions and functions such as controlling aggregation and multi-hopping. The mean residence time of a single particle is found considerably reduced from 7 s, as predicted by Kramer's theory, to 0...
February 26, 2018: Nature Communications
https://www.readbyqxmd.com/read/29392843/which-one-is-bulkier-the-3-5-dimethylphenyl-or-the-2-6-dimethylphenyl-group-development-of-size-complementary-molecular-and-macromolecular-2-rotaxanes
#14
Hiroki Sato, Daisuke Aoki, Toshikazu Takata
We developed novel size-complementary molecular and macromolecular rotaxanes using a 2,6-dimethylphenyl terminal group as the axle-end-cap group in dibenzo-24-crown-8-ether (DB24C8)-based rotaxanes, where the 2,6-dimethylphenyl group was found to be less bulky than the 3,5-dimethylphenyl group. A series of molecular and macromolecular [2]rotaxanes that bear a 2,6-dimethylphenyl group as the axle-end-cap were synthesized using unsubstituted and fluorine-substituted DB24C8. Base-induced decomposition into their constituent components confirmed the occurrence of deslipping, which supports the size-complementarity of these rotaxanes...
April 4, 2018: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/29388424/unveiling-the-fundamental-role-of-temperature-in-rram-switching-mechanism-by-multiscale-simulations
#15
Federico Raffone, Giancarlo Cicero
Even though resistance switching memories (RRAMs) can be potentially employed in a broad variety of fields, such as electronics and brain science, they are still affected by issues that prevent their application in circuitry. These problems are a consequence of the lack of detailed knowledge about the physical processes occurring in the device. In this work, we propose multiscale simulations, combining kinetic Monte Carlo and finite difference methods, to shed light on the yet-unclear switching process occurring in the valence change RRAMs, which are believed to work as a consequence of the drift and diffusion of crystalline defects that act as dopants...
February 28, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29388346/prediction-of-the-pharmacokinetics-of-pravastatin-as-an-oatp-substrate-using-plateable-human-hepatocytes-with-human-plasma-data-and-pbpk-modeling
#16
Jialin Mao, Utkarsh Doshi, Matthew Wright, Cornelis E C A Hop, Albert P Li, Yuan Chen
Plateable human hepatocytes with human plasma were utilized to generate the uptake transporter kinetic data for pravastatin, an organic anion-transporting polypeptide (OATP) transporter substrate. The active hepatic uptake of pravastatin was determined with a Jmax value of 134.4 pmol/min/million cells and Km of 76.77 µM in plateable human hepatocytes with human plasma. The physiologically-based pharmacokinetic (PBPK) model with incorporation of these in vitro kinetic data successfully simulated the i.v. pharmacokinetic profile of pravastatin without applying scaling factor (the mean predicted area under the curve (AUC) is within 1...
April 2018: CPT: Pharmacometrics & Systems Pharmacology
https://www.readbyqxmd.com/read/29347048/distribution-of-randomly-diffusing-particles-in-inhomogeneous-media
#17
Yiwei Li, Osman Kahraman, Christoph A Haselwandter
Diffusion can be conceptualized, at microscopic scales, as the random hopping of particles between neighboring lattice sites. In the case of diffusion in inhomogeneous media, distinct spatial domains in the system may yield distinct particle hopping rates. Starting from the master equations (MEs) governing diffusion in inhomogeneous media we derive here, for arbitrary spatial dimensions, the deterministic lattice equations (DLEs) specifying the average particle number at each lattice site for randomly diffusing particles in inhomogeneous media...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346732/microscopic-theory-of-coupled-slow-activated-dynamics-in-glass-forming-binary-mixtures
#18
Rui Zhang, Kenneth S Schweizer
The Elastically Collective Nonlinear Langevin Equation theory for one-component viscous liquids and suspensions is generalized to treat coupled slow activated relaxation and diffusion in glass-forming binary sphere mixtures of any composition, size ratio, and interparticle interactions. A trajectory-level dynamical coupling parameter concept is introduced to construct two coupled dynamic free energy functions for the smaller penetrant and larger matrix particle. A two-step dynamical picture is proposed where the first-step process involves matrix-facilitated penetrant hopping quantified in a self-consistent manner based on a temporal coincidence condition...
April 5, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29290539/is-acl-reconstruction-a-prerequisite-for-the-patients-having-recreational-sporting-activities
#19
Emrah Kovalak, Tolga Atay, Cem Çetin, I Meltem Atay, Mustafa Onur Serbest
OBJECTIVE: Whether surgical or conservative treatment is more effective in allowing patients to return to physical activity after anterior cruciate ligament (ACL) injury is controversial. We sought to compare mid-term outcome measures between isolated ACL tear patients who underwent reconstruction followed by closed kinetic chain exercises and those who underwent neuromuscular training only. METHODS: We retrospectively evaluated patients with ACL tears who underwent post-surgery CKC strength training after ACL reconstruction (Group A), and patients who only underwent neuromuscular training (Group B) with a minimum follow-up time of 5 years...
January 2018: Acta Orthopaedica et Traumatologica Turcica
https://www.readbyqxmd.com/read/29218993/energy-landscape-of-the-substrate-translocation-equilibrium-of-plasma-membrane-glutamate-transporters
#20
Jiali Wang, Thomas Albers, Christof Grewer
Glutamate transporters maintain a large glutamate concentration gradient across synaptic membranes and are, thus, critical for functioning of the excitatory synapse. Mammalian glutamate transporters concentrate glutamate inside cells through energetic coupling of glutamate flux to the transmembrane concentration gradient of Na+ . Structural models based on an archeal homologue, GltPh, suggest an elevator-like carrier mechanism. However, the energetic determinants of this carrier-based movement are not well understood...
January 11, 2018: Journal of Physical Chemistry. B
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