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25th Annual Computational Neuroscience Meeting: CNS-2016.
Sharpee TO, Destexhe A, Kawato M, Sekulić V, Skinner FK, Wójcik DK, Chintaluri C, Cserpán D, Somogyvári Z, Kim JK, Kilpatrick ZP, Bennett MR, Josić K, Elices I, Arroyo D, Levi R, Rodriguez FB, Varona P, Hwang E, Kim B, Han HB, Kim T, McKenna JT, Brown RE, McCarley RW, Choi JH, Rankin J, Popp PO, Rinzel J, Tabas A, Rupp A, Balaguer-Ballester E, Maturana MI, Grayden DB, Cloherty SL, Kameneva T, Ibbotson MR, Meffin H, Koren V, Lochmann T, Dragoi V, Obermayer K, Psarrou M, Schilstra M, Davey N, Torben-Nielsen B, Steuber V, Ju H, Yu J, Hines ML, Chen L, Yu Y, Kim J, Leahy W, Shlizerman E, Birgiolas J, Gerkin RC, Crook SM, Viriyopase A, Memmesheimer RM, Gielen S, Dabaghian Y, DeVito J, Perotti L, Kim AJ, Fenk LM, Cheng C, Maimon G, Zhao C, Widmer Y, Sprecher S, Senn W, Halnes G, Mäki-Marttunen T, Keller D, Pettersen KH, Andreassen OA, Einevoll GT, Yamada Y, Steyn-Ross ML, Alistair Steyn-Ross D, Mejias JF, Murray JD, Kennedy H, Wang XJ, Kruscha A, Grewe J, Benda J, Lindner B, Badel L, Ohta K, Tsuchimoto Y, Kazama H, Kahng B, Tam ND, Pollonini L, Zouridakis G, Soh J, Kim D, Yoo M, Palmer SE, Culmone V, Bojak I, Ferrario A, Merrison-Hort R, Borisyuk R, Kim CS, Tezuka T, Joo P, Rho YA, Burt… See abstract for full author list ➔ Sharpee TO, et al. BMC Neurosci. 2016 Aug 18;17 Suppl 1(Suppl 1):54. doi: 10.1186/s12868-016-0283-6. BMC Neurosci. 2016. PMID: 27534393 Free PMC article.
Schiff P68 STDP improves speech recognition capabilities in spiking recurrent circuits parameterized via differential evolution Markov Chain Monte Carlo Richard Veale, Matthias Scheutz P69 Bidirectional transformation between dominant cortical neural activities and phase d …
Schiff P68 STDP improves speech recognition capabilities in spiking recurrent circuits parameterized via differential evolution Markov Chain …
Generative models of conformational dynamics.
Langmead CJ. Langmead CJ. Adv Exp Med Biol. 2014;805:87-105. doi: 10.1007/978-3-319-02970-2_4. Adv Exp Med Biol. 2014. PMID: 24446358 Free PMC article. Review.
Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermo …
Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo proc …
PyQMC: An all-Python real-space quantum Monte Carlo module in PySCF.
Wheeler WA, Pathak S, Kleiner KG, Yuan S, Rodrigues JNB, Lorsung C, Krongchon K, Chang Y, Zhou Y, Busemeyer B, Williams KT, Muñoz A, Chow CY, Wagner LK. Wheeler WA, et al. J Chem Phys. 2023 Mar 21;158(11):114801. doi: 10.1063/5.0139024. J Chem Phys. 2023. PMID: 36948839
We describe a new open-source Python-based package for high accuracy correlated electron calculations using quantum Monte Carlo (QMC) in real space: PyQMC. PyQMC implements modern versions of QMC algorithms in an accessible format, enabling algorithmic development and easy …
We describe a new open-source Python-based package for high accuracy correlated electron calculations using quantum Monte Carlo (QMC) …
Visualizing Atomically Layered Magnetism in CrSBr.
Rizzo DJ, McLeod AS, Carnahan C, Telford EJ, Dismukes AH, Wiscons RA, Dong Y, Nuckolls C, Dean CR, Pasupathy AN, Roy X, Xiao D, Basov DN. Rizzo DJ, et al. Adv Mater. 2022 Jul;34(27):e2201000. doi: 10.1002/adma.202201000. Epub 2022 May 31. Adv Mater. 2022. PMID: 35504841
Here, spatially dependent magnetism in few-layer CrSBr is revealed using magnetic force microscopy (MFM) and Monte Carlo-based simulations. Nanoscale visualization of the magnetic sheet susceptibility is extracted from MFM data and force-distance curves, revealing a charac …
Here, spatially dependent magnetism in few-layer CrSBr is revealed using magnetic force microscopy (MFM) and Monte Carlo-based simula …
An introduction to g methods.
Naimi AI, Cole SR, Kennedy EH. Naimi AI, et al. Int J Epidemiol. 2017 Apr 1;46(2):756-762. doi: 10.1093/ije/dyw323. Int J Epidemiol. 2017. PMID: 28039382 Free PMC article.
Monte Carlo renormalization-group calculation for the d=3 Ising model using a modified transformation.
Ron D, Brandt A, Swendsen RH. Ron D, et al. Phys Rev E. 2021 Aug;104(2-2):025311. doi: 10.1103/PhysRevE.104.025311. Phys Rev E. 2021. PMID: 34525628
The iterative method uses a modified block-spin transformation with a tunable parameter to improve convergence in the Monte Carlo renormalization group trajectory. We found experimentally that the iterative method enables the calculation of the critical temperature simulta …
The iterative method uses a modified block-spin transformation with a tunable parameter to improve convergence in the Monte Carlo ren …
Effect of the presence of amniotic fluid for optical transabdominal fetal monitoring using Monte Carlo simulations.
Gunther J, Jayet B, Jacobs A, Burke R, Kainerstorfer JM, Andersson-Engels S. Gunther J, et al. J Biophotonics. 2021 Sep;14(9):e202000486. doi: 10.1002/jbio.202000486. Epub 2021 Jun 19. J Biophotonics. 2021. PMID: 34110703
Current techniques are, however, inefficient at determining fetal distress leading to a high false positive rate for complications and ultimately a C-section. For the current study, Monte Carlo simulations were used to calculate the amount of signal received on a model of …
Current techniques are, however, inefficient at determining fetal distress leading to a high false positive rate for complications and ultim …
Microphysiological Modeling of the Structure and Function of Neuromuscular Transmitter Release Sites.
Laghaei R, Meriney SD. Laghaei R, et al. Front Synaptic Neurosci. 2022 Jun 13;14:917285. doi: 10.3389/fnsyn.2022.917285. eCollection 2022. Front Synaptic Neurosci. 2022. PMID: 35769072 Free PMC article. Review.
MCell provides a powerful simulation approach that employs particle-based stochastic simulation tools to study presynaptic processes in realistic and complex (3D) geometries using optimized Monte Carlo algorithms to track finite numbers of molecules as they diffuse and int …
MCell provides a powerful simulation approach that employs particle-based stochastic simulation tools to study presynaptic processes in real …
A new look at state-space models for neural data.
Paninski L, Ahmadian Y, Ferreira DG, Koyama S, Rahnama Rad K, Vidne M, Vogelstein J, Wu W. Paninski L, et al. J Comput Neurosci. 2010 Aug;29(1-2):107-126. doi: 10.1007/s10827-009-0179-x. Epub 2009 Aug 1. J Comput Neurosci. 2010. PMID: 19649698 Free PMC article. Review.
We close by discussing some applications of this more general point of view, including Markov chain Monte Carlo methods for neural decoding and efficient estimation of spatially-varying firing rates....
We close by discussing some applications of this more general point of view, including Markov chain Monte Carlo methods for neural de …
115 results