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Evaluation of Unrestrained Replica-Exchange Simulations Using Dynamic Walkers in Temperature Space for Protein Structure Refinement

Mark A. Olson, Michael S. Lee, Yang Zhang
2014 PLoS ONE  
To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.  ...  In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population  ...  An alternative adaptive algorithm has been developed based on convective methods to improve efficient sampling of energy basins that are limited by conventional replica-exchange methods [21] .  ... 
doi:10.1371/journal.pone.0096638 pmid:24848767 pmcid:PMC4029997 fatcat:5hhhkoybxbfjjjlrr6jo7linwi

Convective Replica-Exchange in Ergodic Regimes [article]

Giorgio F. Signorini and Edoardo Giovannelli and Yannick G. Spill and Michael Nilges and Riccardo Chelli
2014 arXiv   pre-print
a more effective sampling of energy basins.  ...  In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme.  ...  Acknowledgments We thank Piero Procacci for stimulating discussions and Pierluigi Cresci for technical support. This work was supported by European Union Contract RII3-CT-2003-506350. Y. G.  ... 
arXiv:1307.2115v3 fatcat:xowm44ouxfajvib5vp4bgma6ba

Drought sensitivity of Amazonian carbon balance revealed by atmospheric measurements

L. V. Gatti, M. Gloor, J. B. Miller, C. E. Doughty, Y. Malhi, L. G. Domingues, L. S. Basso, A. Martinewski, C. S. C. Correia, V. F. Borges, S. Freitas, R. Braz (+5 others)
2014 Nature  
Bakwin, who had the foresight to initiate a long-term high-precision greenhouse gas measurement laboratory in Sao Paulo, and D.  ...  METHODS Air sampling and analysis.  ...  Once a vertical profile has been sampled (one suitcase filled) it is transported to the IPEN Atmospheric Chemistry Laboratory in Sao Paulo, where samples are analysed by a replica of the NOAA/ ESRL trace  ... 
doi:10.1038/nature12957 pmid:24499918 fatcat:lhnjvosre5h5ljxwyyysmpwche

Numerical Simulation on Heat Transfer Characteristics of Water Flowing through the Fracture of High-Temperature Rock

Xiaohu Zhang, Zhaolun Wang, Yanhua Sun, Chun Zhu, Feng Xiong, Qiongqiong Tang
2020 Geofluids  
This study provides a reference for enhancing the heat transfer coefficient to benefit the exploitation of heat energy of hot dry rock.  ...  A new heat transfer coefficient was proposed considering aperture size, water flow velocity, and rock fracture roughness.  ...  [17] proposed an analytical method to develop a more effective equation for the HTC based on the temperature distribution in the fracture wall along the direction of the sample radius.  ... 
doi:10.1155/2020/8864028 fatcat:jumidtsny5eafpsrddsi3txxae

Review: Geothermal heat as a tracer of large-scale groundwater flow and as a means to determine permeability fields

Martin O. Saar
2010 Hydrogeology Journal  
A review of coupled groundwater and heat transfer theory is followed by an introduction to geothermal measurement techniques.  ...  Therefore, a wide range of permeabilities can be investigated by analyzing subsurface temperatures or heat discharge at springs.  ...  Support for this contribution and related research is acknowledged from the National Science Foundation (NSF) under Grant Numbers EAR-0838541, DMS-0724560, and EAR-0941666 and from the Department of Energy  ... 
doi:10.1007/s10040-010-0657-2 fatcat:tdsq7bhac5g4heeyg3jcdcdfli

HESS Opinions: Functional units: a novel framework to explore the link between spatial organization and hydrological functioning of intermediate scale catchments

E. Zehe, U. Ehret, L. Pfister, T. Blume, B. Schröder, M. Westhoff, C. Jackisch, S. J. Schymanski, M. Weiler, K. Schulz, N. Allroggen, J. Tronicke (+5 others)
2014 Hydrology and Earth System Sciences Discussions  
A second asset of this framework is that it blueprints a way towards a structurally more adequate model concept for water and energy cycles in intermediate scale catchments, which balances necessary complexity  ...  This opinion paper proposes a novel framework for exploring how spatial organization alongside with spatial heterogeneity controls functioning of intermediate scale catchments of organized complexity.  ...  We also acknowledge support for open access publishing by the Deutsche  ... 
doi:10.5194/hessd-11-3249-2014 fatcat:5gne562dbjbmdmalzptfivi3pq

Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex

Grant Hartung, Shoale Badr, Mohammad Moeini, Frédéric Lesage, David Kleinfeld, Ali Alaraj, Andreas Linninger, Roeland M.H. Merks
2021 PLoS Computational Biology  
Mathematical models informed by spatially and temporally distributed neuroimage data are becoming instrumental for reconstructing a coherent picture of normal and pathological oxygen delivery throughout  ...  The feasibility and accuracy of the novel method is demonstrated and validated with in vivo oxygen perfusion data in cohorts of young and aged mice.  ...  In conclusion, the proposed voxelized technique which requires no mesh generation offers a scalable method for performing computer simulations of solute exchange and metabolism for sizable sections of  ... 
doi:10.1371/journal.pcbi.1008584 pmid:33507970 fatcat:htvjqnhjpzer7dmoahicgx7jou

Kinetic roughening phenomena, stochastic growth, directed polymers and all that. Aspects of multidisciplinary statistical mechanics

Timothy Halpin-Healy, Yi-Cheng Zhang
1995 Physics reports  
, infinite matrix products, Burgers equation for shock waves, Kuromato-Sivashinski equation for flame propagation, passive scalars in turbulent fluids, selforganized criticality, spin glasses, replica  ...  Being linear, the EW equation is readily solved via Fourier methods.  ...  Acknowledgments This review started with a suggestion by Itamar Procaccia a couple of years ago.  ... 
doi:10.1016/0370-1573(94)00087-j fatcat:kwz2xwvx2zaxdbawslxuq5jij4

National Academy of Sciences: Abstracts of Papers Presented at the Autumn Meeting, October 9-12, 1950, General Electric Company Research Laboratory, Schenectady, New York

1950 Science  
Geologic evidence is consistent with a growing contrast between continental masses and ocean basins and a progressive sinking of the ocean basins, which would mean an in- creasing volume of sea water.  ...  Although there has been improve- ment in the methods used in measuring model forces, little has been done in the development of new methods of measuring quickly and accurately the many pressures of interest  ... 
doi:10.1126/science.112.2912.447 pmid:17779715 fatcat:ngtdjtnqozek7e7jayomzqg2wm

Using Machine Learning at Scale in HPC Simulations with SmartSim: An Application to Ocean Climate Modeling [article]

Sam Partee, Matthew Ellis, Alessandro Rigazzi, Scott Bachman, Gustavo Marques, Andrew Shao, Benjamin Robbins
2021 arXiv   pre-print
SmartSim is a library dedicated to enabling online analysis and Machine Learning (ML) for traditional HPC simulations.  ...  In total, 970 billion inferences are collectively served by running the ensemble for a total of 120 simulated years.  ...  ACKNOWLEDGMENT The authors would like to acknowledge Elliot Ronaghan for his help with application performance, and RedisLabs for their continued support.  ... 
arXiv:2104.09355v1 fatcat:cw7m6p7kk5et7pd23uiueuip6m

Processes that drive the population structuring of Jenynsia lineata (Cyprinidontiformes, Anablepidae) in the La Plata Basin

Yanina F. Briñoccoli, Luiz Jardim de Queiroz, Sergio Bogan, Ariel Paracampo, Paula E. Posadas, Gustavo M. Somoza, Juan I. Montoya‐Burgos, Yamila P. Cardoso
2021 Ecology and Evolution  
: (a) La Plata/Desaguadero Rivers (sampling sites across Argentina, Uruguay, and Southern Brazil), (b) Central Argentina, and (c) Northern Argentina.  ...  And these processes in turn are the basis for possible speciation events.  ...  Latitude (representing IBE): For J. lineata, each sampling site has a coordinate measured in decimals, both for latitude and longitude.  ... 
doi:10.1002/ece3.7427 pmid:34141207 pmcid:PMC8207347 fatcat:mdrly27omrfo7jq4kqb2fgfqi4

Sediment delivery and lake dynamics in a Mediterranean mountain watershed: Human-climate interactions during the last millennium (El Tobar Lake record, Iberian Range, Spain)

Fernando Barreiro-Lostres, Erik Brown, Ana Moreno, Mario Morellón, Mark Abbott, Aubrey Hillman, Santiago Giralt, Blas Valero-Garcés
2015 Science of the Total Environment  
Schnurenberger, A. Norens and M.  ...  Shapley (Limnological Research Center) for the 2004 field expedition to collect the cores, and the Regional Government (Junta de Comunidades de Castilla-La Mancha) for logistic support.  ...  Exchanges of carbon between the sample and the atmosphere are a common cause of contamination in wood.  ... 
doi:10.1016/j.scitotenv.2015.06.123 pmid:26186465 fatcat:xgoaqyut7bcaxlgoqqdkwbbixi

Synthesis meets theory: Past, present and future of rational chemistry

Mauro Fianchini
2017 Physical Sciences Reviews  
Nonetheless, the birth of the scientific method, the technical and technological advances (exploiting revolutionary discoveries in physics) and the improved management and sharing of growing databases  ...  greatly contributed to the evolution of chemistry from an esoteric ground into a mature scientific discipline during these last 400 years.  ...  The next rung in the ladder introduces a degree of non-locality by replacing some local exchange energy density with exact HF exchange energy density; these methods are called hybrid GGAs (rung 4, Table  ... 
doi:10.1515/psr-2017-0134 fatcat:wzsmnadblfhrjapnjujb7tb6aq


1978 Bulletin of The American Meteorological Society - (BAMS)  
Effects of particulate complex refractive index and particle-size distribution variations on atmospheric extinction and absorption for visible through middle IR wavelengths.  ...  The higher sea-surface temperature gives the energy for the convective motion.  ...  A new method was developed to determine the deposition coefficient of water vapor on clean, cleaved surfaces of single ice crystals.  ... 
doi:10.1175/1520-0477-59.4.461 fatcat:jvk27wtrefel7hiajjfr5g2wvi

Controlled Experiments of Hillslope Coevolution at the Biosphere 2 Landscape Evolution Observatory: Toward Prediction of Coupled Hydrological, Biogeochemical, and Ecological Change [chapter]

Till H. M. Volkmann, Aditi Sengupta, Luke A. Pangle, Katerina Dontsova, Greg A. Barron-Gafford, Ciaran J. Harman, Guo-Yue Niu, Laura K. Meredith, Nate Abramson, Antonio A. Meira Neto, Yadi Wang, John R. Adams (+23 others)
2018 Hydrology of Artificial and Controlled Experiments  
This chapter describes the model systems and associated research facilities and illustrates how LEO allows for tracking of multiscale matter and energy fluxes at a level of detail impossible in field experiments  ...  Understanding the process interactions and feedbacks among water, porous geological media, microbes, and vascular plants is crucial for improving predictions of the response of Earth's critical zone to  ...  acknowledge support from the Philecology Foundation of Fort Worth Texas, the National Science Foundation (NSF; NSF-funded project 1344552, NSF-funded Hydrologic Synthesis Project: Water cycle dynamics in a  ... 
doi:10.5772/intechopen.72325 fatcat:ygp74grkk5b2beg4x67nkawcva
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