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https://www.readbyqxmd.com/read/29145413/diffusion-based-neuromodulation-can-eliminate-catastrophic-forgetting-in-simple-neural-networks
#1
Roby Velez, Jeff Clune
A long-term goal of AI is to produce agents that can learn a diversity of skills throughout their lifetimes and continuously improve those skills via experience. A longstanding obstacle towards that goal is catastrophic forgetting, which is when learning new information erases previously learned information. Catastrophic forgetting occurs in artificial neural networks (ANNs), which have fueled most recent advances in AI. A recent paper proposed that catastrophic forgetting in ANNs can be reduced by promoting modularity, which can limit forgetting by isolating task information to specific clusters of nodes and connections (functional modules)...
2017: PloS One
https://www.readbyqxmd.com/read/29144758/on-the-density-dependence-of-the-integral-equation-coarse-graining-effective-potential
#2
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/29144280/selective-ion-permeation-through-strained-and-charged-graphene-membranes
#3
Kun Li, Yi Tao, Zhongwu Li, Jingjie Sha, Yunfei Chen
By means of molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we demonstrate that stretched and charged graphene can act as ion sieve membranes. It is observed that loading 30% strain on graphene can induce pores in the dense electron cloud to allow ions to pass through the aromatic rings. Meanwhile, charged surface is helpful to peel the hydration layers from the ions and decrease the energy barrier for ion translocation through nanopores. Our results suggest that with membrane charge density of 6...
November 16, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29143010/exploring-what-prompts-itic-to-become-a-superior-acceptor-in-organic-solar-cell-by-combining-molecular-dynamics-simulation-with-quantum-chemistry-calculation
#4
Qing-Qing Pan, Shuang-Bao Li, Ying-Chen Duan, Yong Wu, Ji Zhang, Yun Geng, Liang Zhao, Zhong-Min Su
The interface characteristic is a crucial factor determining the power conversion efficiency of organic solar cells (OSCs). In this work, our aim is to conduct a comparative study on the interface characteristics between the very famous non-fullerene acceptor, ITIC, and a fullerene acceptor, PC71BM by combining molecular dynamics simulations with density functional theory. Based on some typical interface models of the acceptor ITIC or PC71BM and the donor PBDB-T selected from MD simulation, besides the evaluation of charge separation/recombination rates, the relative positions of Frenkel exciton (FE) states and the charge transfer states along with their oscillator strengths are also employed to estimate the charge separation abilities...
November 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29141589/reconstructing-cancer-karyotypes-from-short-read-data-the-half-empty-and-half-full-glass
#5
Rami Eitan, Ron Shamir
BACKGROUND: During cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a highly complex, patient-specific cancer karyotype. Using high-throughput technologies of deep sequencing and microarrays it is possible to interrogate a cancer genome and produce chromosomal copy number profiles and a list of breakpoints ("jumps") relative to the normal genome...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29141436/surface-hopping-dynamics-including-intersystem-crossing-using-the-algebraic-diagrammatic-construction-method
#6
Sebastian Mai, Felix Plasser, Mathias Pabst, Frank Neese, Andreas Köhn, Leticia González
We report an implementation for employing the algebraic diagrammatic construction to second order [ADC(2)] ab initio electronic structure level of theory in nonadiabatic dynamics simulations in the framework of the SHARC (surface hopping including arbitrary couplings) dynamics method. The implementation is intended to enable computationally efficient, reliable, and easy-to-use nonadiabatic dynamics simulations of intersystem crossing in organic molecules. The methodology is evaluated for the 2-thiouracil molecule...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29140696/attosecond-x-ray-diffraction-triggered-by-core-or-valence-ionization-of-a-dipeptide
#7
Daeheum Cho, Jeremy R Rouxel, Markus Kowalewski, Jin Yong Lee, Shaul Mukamel
With the advancement of high quality X-ray sources, it is now possible to create a molecular movie by following the electronic dynamics in real-time and real-space through time resolved X-ray diffraction. Here, we employ real-time time-dependent density functional theory (RT-TDDFT) to simulate the electronic dynamics after an impulse core or valence ionization in the glycine-phenylalanine (GF) dipeptide. The simulation yields the time-evolving dipole moment, the charge density, and the time-resolved X-ray diffraction signals...
November 15, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29140090/qm-mm-simulations-identify-the-ring-opening-mechanism-of-creatininase
#8
Jitrayut Jitonnom, Joni Mujika, Marc W van der Kamp, Adrian J Mulholland
Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water-addition followed by ring-opening. Water-addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring-opening is still under debate. The proton donor in this step is either His178, or a water molecule bound to one of metal ions, and the roles of His178 and Glu122 are unclear. Here, the two possible reaction pathways have been fully examined by means of combined quantum mechanics/molecular mechanics simulations at the SCC-DFTB/CHARMM22 level of theory...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29139509/nexafs-spectroscopy-of-ionic-liquids-experiments-versus-calculations
#9
Richard M Fogarty, Richard P Matthews, Matthew T Clough, Claire R Ashworth, Agnieszka Brandt-Talbot, Paul J Corbett, Robert G Palgrave, Richard A Bourne, Thomas W Chamberlain, Tom Vander Hoogerstraete, Paul B J Thompson, Patricia A Hunt, Nicholas A Besley, Kevin R J Lovelock
Experimental near edge X-ray absorption fine structure (NEXAFS) spectra are reported for 12 ionic liquids (ILs) encompassing a range of chemical structures for both the sulfur 1s and nitrogen 1s edges and compared with time-dependent density functional theory (TD-DFT) calculations. The energy scales for the experimental data were carefully calibrated against literature data. Gas phase calculations were performed on lone ions, ion pairs and ion pair dimers, with a wide range of ion pair conformers considered...
November 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29138786/electroconvection-of-pure-nematic-liquid-crystals-without-free-charge-carriers
#10
Kuang-Wu Lee, Thorsten Pöschel
We consider electroconvection as a response of nematic liquid crystals to an external electric AC field, in the absence of free charge carriers. Previous experimental and theoretical results emphasized charge carriers as a necessary precondition of electroconvection because free-charges in the fluid can respond to an external electric field. Therefore, ionized molecules are considered as responsible for the driving of electroconvective flows. In experiments, finite conductivity is achieved by adding charge-carrying dye molecules or in non-dyed liquid crystals by impurities of the samples...
November 15, 2017: Soft Matter
https://www.readbyqxmd.com/read/29138311/intrusion-and-extrusion-of-water-in-hydrophobic-nanopores
#11
Antonio Tinti, Alberto Giacomello, Yaroslav Grosu, Carlo Massimo Casciola
Heterogeneous systems composed of hydrophobic nanoporous materials and water are capable, depending on their characteristics, of efficiently dissipating (dampers) or storing ("molecular springs") energy. However, it is difficult to predict their properties based on macroscopic theories-classical capillarity for intrusion and classical nucleation theory (CNT) for extrusion-because of the peculiar behavior of water in extreme confinement. Here we use advanced molecular dynamics techniques to shed light on these nonclassical effects, which are often difficult to investigate directly via experiments, owing to the reduced dimensions of the pores...
November 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29137720/improving-surgical-residents-communication-in-disclosing-complications-a-qualitative-analysis-of-simulated-physician-and-patient-surrogate-conversations
#12
Carolina Fernandez Branson, Jeffrey G Chipman
BACKGROUND: In this study, we explore surgical resident communication with simulated patient surrogates (SPs), in an Objective Structured Clinical Examination (OSCE). METHODS: We use discourse analysis (DA), a qualitative approach to analyzing language, to evaluate our residents' interactions with simulated patient surrogates. After identifying problematic communication patterns, we apply communication theory to discuss our findings and provide suggestions for improvement...
November 7, 2017: American Journal of Surgery
https://www.readbyqxmd.com/read/29137165/abs-fishcount-an-agent-based-simulator-of-underwater-sensors-for-measuring-the-amount-of-fish
#13
Iván García-Magariño, Raquel Lacuesta, Jaime Lloret
Underwater sensors provide one of the possibilities to explore oceans, seas, rivers, fish farms and dams, which all together cover most of our planet's area. Simulators can be helpful to test and discover some possible strategies before implementing these in real underwater sensors. This speeds up the development of research theories so that these can be implemented later. In this context, the current work presents an agent-based simulator for defining and testing strategies for measuring the amount of fish by means of underwater sensors...
November 13, 2017: Sensors
https://www.readbyqxmd.com/read/29136471/below-room-temperature-c-h-bond-breaking-on-an-inexpensive-metal-oxide-methanol-to-formaldehyde-on-ceo2-111
#14
Jonathan E Sutton, Thomas Danielson, Ariana Beste, Aditya Savara
Upgrading of primary alcohols by C-H bond breaking currently requires temperatures of >200 °C. In this work, new understanding from simulation of a temperature-programmed reaction study with methanol over a CeO2(111) surface shows C-H bond breaking and the subsequent desorption of formaldehyde, even below room temperature. This is of particular interest because CeO2 is a naturally abundant and inexpensive metal oxide. We combine density functional theory and kinetic Monte Carlo methods to show that the low-temperature C-H bond breaking occurs via disproportionation of adjacent methoxy species...
November 15, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29136379/rotational-diffusion-propagator-of-the-intramolecular-proton-proton-vector-in-liquid-water-a-molecular-dynamics-study
#15
Wisman Acharige Monika Madhavi, M S Samantha Weerasinghe, Konstantin I Momot
Rotational motion of water molecules plays the dominant role in determining NMR spin relaxation properties of liquid water and many biological tissues. The traditional theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of water molecules is described by a continuous-time rotational-diffusion random walk with a single rotational diffusion coefficient. However, recent experimental and theoretical studies have demonstrated that water reorientation occurs via large, discrete angle jumps superimposed on a continuous-time rotational diffusion process...
November 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29136363/dynamic-stabilization-of-the-ligand-metal-interface-in-atomically-precise-gold-nanoclusters-au68-and-au144-protected-by-meta-mercaptobenzoic-acid
#16
Tiia-Riikka Tero, Sami Malola, Benedek Koncz, Emmi Pohjolainen, Saara Lautala, Satu Mustalahti, Perttu Permi, Gerrit Groenhof, Mika Pettersson, Hannu Häkkinen
Ligand-stabilized, atomically precise gold nanoclusters with a metal core of a uniform size of just 1 - 3 nm constitute an interesting class of nanomaterials with versatile possibilities for applications due to their size dependent properties and modifiable ligand layers. The key to extending the usability of the clusters in applications is to understand the chemical bonding in the ligand layer as a function of cluster size and ligand structure. Previously, it has been shown that monodispersed gold nanoclusters, stabilized by meta-mercaptobenzoic acid (m-MBA or 3-MBA) ligands and with sizes of 68 to 144 gold atoms, show ambient stability...
November 14, 2017: ACS Nano
https://www.readbyqxmd.com/read/29136070/atomistic-potential-for-graphene-and-other-sp-2-carbon-systems
#17
Zacharias G Fthenakis, George Kalosakas, Georgios D Chatzidakis, Costas Galiotis, Konstantinos Papagelis, Nektarios N Lathiotakis
We introduce a torsional force field for sp(2) carbon to augment an in-plane atomistic potential of a previous work [G. Kalosakas et al., J. Appl. Phys., 2013, 113, 134307] so that it is applicable to out-of-plane deformations of graphene and related carbon materials. The introduced force field is fit to reproduce density-functional-theory calculation data of appropriately chosen structures. The aim is to create a force field that is as simple as possible so it can be efficient for large scale atomistic simulations of various sp(2) carbon structures without significant loss of accuracy...
November 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29135470/planar-screening-by-charge-polydisperse-counterions
#18
Martin Trulsson, Emmanuel Trizac, Ladislav Samaj
We study how a neutralising cloud of counterions screens the electric field of a uniformly charged planar membrane (plate), when the counterions are characterised by a distribution of charges (or valence), n(q). We work out analytically the one-plate and two-plate cases, at the level of non-linear Poisson-Boltzmann theory. The (essentially asymptotic) predictions are successfully compared to numerical solutions of the full Poisson-Boltzmann theory, but also to Monte Carlo simulations...
November 14, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29135256/improved-solution-state-properties-of-monoclonal-antibodies-by-targeted-mutations
#19
Alexander B Kuhn, Sebastian Kube, Anne R Karow-Zwick, Daniel Seeliger, Patrick Garidel, Michaela Blech, Lars V Schäfer
Monoclonal antibody (mAb) based therapeutics often require high concentration formulations. Unfortunately, highly concentrated antibody solutions often have biophysical properties that are disadvantageous for therapeutic development, such as high viscosity, solubility limitations, precipitation issues, or liquid-liquid phase separation. In this work, we present a computational rational design principle for improving the thermodynamic stability of mAb solutions through targeted point mutations. Two publicly available IgG1 monoclonal antibodies that exhibit high viscosity at high concentrations were used as model systems...
November 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29135220/strong-influence-of-ti-adhesion-layer-on-electron-phonon-relaxation-in-thin-gold-films-ab-initio-nonadiabatic-molecular-dynamics
#20
Xin Zhou, Joanna Jankowska, Linqiu Li, Ashutosh Giri, Patrick E Hopkins, Oleg V Prezhdo
Electron-phonon relaxation in thin metal films is an important consideration for many ultra-small devices and ultra-fast applications. Recent time-resolved experiments demonstrate a significant, more than a factor of five, increase in the electron-phonon coupling and an acceleration in the electron-phonon relaxation rate when a narrow Ti adhesion layer is introduced between an Au film and a non-metal substrate. Using nonadiabatic molecular dynamics combined with real-time time-dependent density functional theory, we identify the reasons that give rise to this strong effect...
November 14, 2017: ACS Applied Materials & Interfaces
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