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Theory of simulation

Brian Kolb, Xuan Luo, Xueyao Zhou, Bin Jiang, Hua Guo
Ab initio molecular dynamics (AIMD) simulations of molecule-surface scattering allow first-principles characterization of the dynamics. However, the large number of density functional theory calculations along the trajectories are very costly, limiting simulations of long-time events. To avoid this computational bottleneck, we report here the development of a high-dimensional molecule-surface interaction potential energy surface (PES) with movable surface atoms, using a machine learning approach. With 60 degrees of freedom, this PES allows energy transfer between the impinging molecule and surface atoms...
January 19, 2017: Journal of Physical Chemistry Letters
Devarajan Sridharan, Nicholas A Steinmetz, Tirin Moore, Eric I Knudsen
: Distinct networks in the forebrain and the midbrain coordinate to control spatial attention. The critical involvement of the superior colliculus (SC)-the central structure in the midbrain network-in visuospatial attention has been shown by four seminal, published studies in monkeys (Macaca mulatta) performing multialternative tasks. However, due to the lack of a mechanistic framework for interpreting behavioral data in such tasks, the nature of the SC's contribution to attention remains unclear...
January 18, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Pan Li, Shan Jiang, Dong Liang, Zhiyong Yang, Yan Yu, Wei Wang
Steerable needles can potentially improve the effectiveness of diagnostic and therapeutic procedures, such as biopsy and cancer treatment, by increasing the targeting accuracy and reaching previously inaccessible targets. A discrete potential field algorithm based on three dimensional (3D) anatomical structures is proposed in this paper to plan the needle path in minimally invasive surgery. A 3D kinematic model of needle steering is formulated using Lie group theory. Model parameters are fitted using experimental data acquired via a 2-degree of freedom robotic device and an ultrasound imaging device...
January 16, 2017: Medical Engineering & Physics
Raphael Hellwig, Tobias Paintner, Zhi Chen, Mario Ruben, Ari P Seitsonen, Florian Klappenberger, Harald Brune, Johannes V Barth
We report on the surface-guided synthesis of an unprecedented dinuclear organocobalt complex, its self-assembly into a complex nanoarchitecture, and a single-molecule level investigation of its switching behavior. Initially, an organic layer is prepared by depositing hexakis((trimethylsilyl)ethynyl)-benzene under ultra-high vacuum conditions onto Ag(111). After Co dosage at 200 Kelvin, low-temperature scanning tunneling microscopy (STM) reveals an epitaxy-mediated organization mechanism of molecules and on-surface formed host-guest complexes...
January 18, 2017: ACS Nano
Biswajit Biswas, Saptarsi Mondal, Prashant Chandra Singh
Presence of the fluorocarbon group in fluorinated alcohols makes them an important class of molecules which have diverse applications in the field of separation techniques, synthetic chemistry, polymer industry, and biology. In this paper, we have performed the density function theory calculation along with atom in molecule analysis, molecular dynamics simulation as well as IR measurements of the bulk mono fluoro-ethanol (MFE) and compared them with the bulk ethanol (ETH) in order to understand the effect of fluorocarbon group in the structure as well as hydrogen bond network of the bulk MFE...
January 18, 2017: Journal of Physical Chemistry. A
Elvar Ö Jónsson, Susi Lehtola, Martti Puska, Hannes Jónsson
The theory for the generation of Wannier functions within the generalized Pipek-Mezey approach (Lehtola, S.; Jónsson, H. J. Chem. Theory Comput. 2014, 10, 642) is presented and an implementation thereof is described. Results are shown for systems with periodicity in one, two, and three dimensions as well as isolated molecules. The generalized Pipek-Mezey Wannier functions (PMWF) are highly localized orbitals consistent with chemical intuition where a distinction is maintained between σ- and π-orbitals. The PMWF method is compared with the so-called maximally localized Wannier functions (MLWFs) that are frequently used for the analysis of condensed matter calculations...
January 18, 2017: Journal of Chemical Theory and Computation
Zhaowei Wang, Peng Zeng, Mingtuo Zhou, Dong Li, Jintao Wang
Time synchronization is one of the key technologies in Industrial Wireless Sensor Networks (IWSNs), and clustering is widely used in WSNs for data fusion and information collection to reduce redundant data and communication overhead. Considering IWSNs' demand for low energy consumption, fast convergence, and robustness, this paper presents a novel Cluster-based Maximum consensus Time Synchronization (CMTS) method. It consists of two parts: intra-cluster time synchronization and inter-cluster time synchronization...
January 13, 2017: Sensors
Kristina Pickl, Jayant Pande, Harald Köstler, Ulrich Rüde, Ana-Suncana Smith
Propulsion at low Reynolds numbers is often studied by defining artificial microswimmers which exhibit a particular stroke. The disadvantage of such an approach is that the stroke does not adjust to the environment, in particular the fluid flow, which can diminish the effect of hydrodynamic interactions. To overcome this limitation, we simulate a microswimmer consisting of three beads connected by springs and dampers, using the self-developed waLBerla and <i>pe</i> framework based on the lattice Boltzmann method and the discrete element method...
January 18, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Hyun Woo Cho, Bong June Sung
We investigate the glass transition and interfacial dynamics of single strand fibers of flexible polymers by employing molecular dynamics (MD) simulations along with a coarse grained model. While the polymer fiber has drawn significant attention due to its applicability in tissue engineering and stretchable electronics, its dynamic properties, especially the glass transition temperature (Tg), are yet to be understood at the molecular level. For example, there has been a controversy on the effect of the polymer fiber radius (R) on Tg: Tg decreased with a decrease in R for some polymer fibers, whereas Tg of other polymer fibers was not sensitive to R...
January 18, 2017: Soft Matter
Fei Sun, Sailing He
A novel thermal lens that can achieve a remote cooling effect is designed by transformation thermodynamics. The effective distance between the separate hot source and cold source is shortened by our shelled thermal lens without any negative thermal conductivity. Numerical simulations verify the performance of our thermal lens. Based on the effective medium theory, we also propose a practical way to realize our lens using two-layered isotropic thermal media that are both found in nature. The proposed thermal lens will have potential applications in remote temperature control and in creating other thermal illusions...
January 18, 2017: Scientific Reports
Maurits K Konings, Roland A Snijder, Joris H Radermacher, Annemoon M Timmerman
BACKGROUND: In this paper, a new method is presented that combines mechanical compliance effects with Poiseuille flow and push-out effects ("dead volume") in one single mathematical framework for calculating dosing errors in multi-infusion set-ups. In contrast to existing numerical methods, our method produces explicit expressions that illustrate the mathematical dependencies of the dosing errors on hardware parameters and pump flow rate settings. METHODS: Our new approach uses the Z-transform to model the contents of the catheter, and after implementation in Mathematica (Wolfram), explicit expressions are produced automatically...
January 17, 2017: Biomedical Engineering Online
Yoshua Bengio, Thomas Mesnard, Asja Fischer, Saizheng Zhang, Yuhuai Wu
We show that Langevin Monte Carlo Markov chain inference in an energy-based model with latent variables has the property that the early steps of inference, starting from a stationary point, correspond to propagating error gradients into internal layers, similar to backpropagation. The backpropagated error is with respect to output units that have received an outside driving force pushing them away from the stationary point. Backpropagated error gradients correspond to temporal derivatives with respect to the activation of hidden units...
January 17, 2017: Neural Computation
Oscar Oviedo-Trespalacios, Md Mazharul Haque, Mark King, Simon Washington
OBJECTIVE: The adaptive behaviour of mobile phone distracted drivers has been a topic of much discussion in the recent literature. Both simulator and naturalistic studies suggests that distracted drivers generally select lower driving speeds; however, speed adaptation is not observed among all drivers, and the mechanisms of speed selection are not well understood. The aim of this research was to apply a driver behavioural adaptation model to investigate the speed adaptation of mobile phone distracted drivers...
January 17, 2017: Traffic Injury Prevention
Mehdi Keramati, Audrey Durand, Paul Girardeau, Boris Gutkin, Serge H Ahmed
Drug addiction implicates both reward learning and homeostatic regulation mechanisms of the brain. This has stimulated 2 partially successful theoretical perspectives on addiction. Many important aspects of addiction, however, remain to be explained within a single, unified framework that integrates the 2 mechanisms. Building upon a recently developed homeostatic reinforcement learning theory, the authors focus on a key transition stage of addiction that is well modeled in animals, escalation of drug use, and propose a computational theory of cocaine addiction where cocaine reinforces behavior due to its rapid homeostatic corrective effect, whereas its chronic use induces slow and long-lasting changes in homeostatic setpoint...
January 16, 2017: Psychological Review
Emanuele Maggio, Peitao Liu, Michiel J van Setten, Georg Kresse
In a recent work, van Setten and coworkers have presented a carefully converged G0W0 study of 100 closed shell molecules [J. Chem. Theory Comput. 2015, 11, 5665-5687]. For two different codes they found excellent agreement to within few 10 meV if identical Gaussian basis sets were used. We inspect the same set of molecules using the projector augmented wave method and the Vienna ab initio simulation package (VASP). For the ionization potential, the basis set extrapolated plane wave results agree very well with the Gaussian basis sets, often reaching better than 50 meV agreement...
January 17, 2017: Journal of Chemical Theory and Computation
Ying-Chen Duan, Yong Wu, Jun-Ling Jin, Dong-Mei Gu, Yun Geng, Min Zhang, Zhongmin Su
The case that aggregation brings a huge influence on the structure and fluorescent property of 5-(4-(1,2,2-triphenylvinyl)phenyl)thiophene-2-carbaldehyde (P4TA) was detailedly investigated here by employing both quantum mechanics and molecular mechanics. Besides the isolated molecule, the aggregated molecule both in water and crystal state was studied by focusing on the comparison of photoelectronic properties, including the geometrical and electronic structures at ground and excited states, emission and internal conversation properties...
January 17, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Priyanka Garg, Indrani Choudhuri, Arup Mahata, Biswarup Pathak
Stanene is a quantum spin Hall insulator and a promising material for electronic and optoelectronic devices. Density functional theory (DFT) calculations are performed to study the band gap opening in stanene by elemental mono-doping (B, N) and co-doping (B-N). Different patterned B-N co-doping is studied to change the electronic properties of stanene. A patterned B-N co-doping opens the band gap in stanene and its semiconducting nature persists under strain. Molecular dynamics (MD) simulations are performed to confirm the thermal stability of such a doped system...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
Chi Chen, Ziheng Lu, Francesco Ciucci
Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps...
January 17, 2017: Scientific Reports
Claudia Stephan, Klaus Zuberbühler
Sexual dimorphisms in animal vocal behavior have been successfully explained by sexual selection theory (e.g., mammals [1-5]; birds [6, 7]; anurans [8, 9]), but this does not usually include alarm calls, which are thought to be the product of kin or individual selection (e.g., [10, 11]). Here, we present the results of playback experiments with wild Diana monkeys, a species with highly dimorphic predator-specific alarms, to investigate the communication strategies of males and females during predator encounters...
November 7, 2016: Current Biology: CB
Xiangyang Zhou, Beilei Zhao, Wei Liu, Haixiao Yue, Ruixia Yu, Yulong Zhao
A compound scheme is proposed to compensate the effect of nonlinear friction disturbance on the control precision of a three-axis inertially stabilized platform (ISP) for aerial remote sensing applications. The scheme consists of friction parameters identification and adaptive compensation. A LuGre model-based ISP friction model is first developed. Then, a comprehensive experimental scheme is proposed to obtain the static friction parameters. Further, the dynamic parameters are identified by experiments and dynamic optimization...
January 13, 2017: ISA Transactions
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