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  • 1
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    Non-equilibrium simulations of thermally induced electric fields in water (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-06-11
    Description: Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 10 7 and 5 × 10 7 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139 , 014504 (2013); J. Armstrong et al. , J. Chem. Phys. 143 , 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    An enhanced version of the heat exchange algorithm with excellent energy conservation properties (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-09-26
    Description: We propose a new algorithm for non-equilibrium molecular dynamics simulations of thermal gradients. The algorithm is an extension of the heat exchange algorithm developed by Hafskjold et al. [Mol. Phys. 80 , 1389 (1993); 81 , 251 (1994)], in which a certain amount of heat is added to one region and removed from another by rescaling velocities appropriately. Since the amount of added and removed heat is the same and the dynamics between velocity rescaling steps is Hamiltonian, the heat exchange algorithm is expected to conserve the energy. However, it has been reported previously that the original version of the heat exchange algorithm exhibits a pronounced drift in the total energy, the exact cause of which remained hitherto unclear. Here, we show that the energy drift is due to the truncation error arising from the operator splitting and suggest an additional coordinate integration step as a remedy. The new algorithm retains all the advantages of the original one whilst exhibiting excellent energy conservation as illustrated for a Lennard-Jones liquid and SPC/E water.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Living Clusters and Crystals from Low-Density Suspensions of Active Colloids (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-12-12
    Description: Author(s): B. M. Mognetti, A. Šarić, S. Angioletti-Uberti, A. Cacciuto, C. Valeriani, and D. Frenkel Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In ... [Phys. Rev. Lett. 111, 245702] Published Wed Dec 11, 2013
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    Transdisciplinary EU science institute needs funds urgently (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vasbinder, Jan W -- Andersson, Bertil -- Arthur, W Brian -- Boasson, Maarten -- de Boer, Rob -- Changeux, Jean Pierre -- Domingo, Esteban -- Eigen, Manfred -- Fersht, Alan -- Frenkel, Daan -- Rees, Martin -- Groen, Theo -- Huber, Robert -- Hunt, Tim -- Holland, John -- May, Robert -- Norrby, Erling -- Nijkamp, Peter -- Lehn, Jean Marie -- Rabbinge, Rudy -- Scheffer, Marten -- Schuster, Peter -- Serageldin, Ismail -- Stuip, Jan -- de Vries, Jan -- van Vierssen, Wim -- Willems, Rein -- England -- Nature. 2010 Feb 18;463(7283):876. doi: 10.1038/463876a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164899" target="_blank"〉PubMed〈/a〉
    Keywords: Academies and Institutes/*economics/trends ; Conservation of Natural Resources/economics/trends ; European Union ; Humans ; Internationality ; Netherlands ; Research/*economics/trends ; *Research Design
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Enhancement of protein crystal nucleation by critical density fluctuations (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-09-26
    Description: Numerical simulations of homogeneous crystal nucleation with a model for globular proteins with short-range attractive interactions showed that the presence of a metastable fluid-fluid critical point drastically changes the pathway for the formation of a crystal nucleus. Close to this critical point, the free-energy barrier for crystal nucleation is strongly reduced and hence, the crystal nucleation rate increases by many orders of magnitude. Because the location of the metastable critical point can be controlled by changing the composition of the solvent, the present work suggests a systematic approach to promote protein crystallization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉ten Wolde, P R -- Frenkel, D -- New York, N.Y. -- Science. 1997 Sep 26;277(5334):1975-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9302288" target="_blank"〉PubMed〈/a〉
    Keywords: Colloids ; Computer Simulation ; Crystallization ; Monte Carlo Method ; Proteins/*chemistry ; Solvents ; Temperature ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Colloidal systems. Playing tricks with designer "atoms" (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frenkel, Daan -- New York, N.Y. -- Science. 2002 Apr 5;296(5565):65-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, Netherlands. frenkel@amolf.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11935011" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Materials science. Colloidal encounters: a matter of attraction (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frenkel, Daan -- New York, N.Y. -- Science. 2006 Nov 3;314(5800):768-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098SJ Amsterdam, Netherlands. frenkel@amolf.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17082442" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Ab initio calculation of the sound velocity of dense hydrogen: implications for models of Jupiter (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-09-01
    Description: First-principles molecular dynamics simulations were used to calculate the sound velocity of dense hydrogen, and the results were compared with extrapolations of experimental data that currently conflict with either astrophysical models or data obtained from recent global oscillation measurements of Jupiter. Excellent agreement with the extrapolated experimental data was obtained. These results strongly support the notion that the existing models for the jovian interior need to be revised.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alavi, A -- Parrinello, M -- Frenkel, D -- New York, N.Y. -- Science. 1995 Sep 1;269(5228):1252-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Cambridge, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7652571" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; *Extraterrestrial Environment ; *Hydrogen ; *Jupiter ; Physicochemical Phenomena ; Pressure ; Temperature ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Theoretical Prediction of Thermal Polarization (2018)
    American Physical Society (APS)
    Details
    Publication Date: 2018-06-02
    Description: Author(s): P. Wirnsberger, C. Dellago, D. Frenkel, and A. Reinhardt We present a mean-field theory to explain the thermo-orientation effect in an off-center Stockmayer fluid. This effect is the underlying cause of thermally induced polarization and thermally induced monopoles, which have recently been predicted theoretically. Unlike previous theories that are based ... [Phys. Rev. Lett. 120, 226001] Published Fri Jun 01, 2018
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 10
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    ChiTaRS-3.1--the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database ( http://chitars.md.biu.ac.il ) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922 chimeric transcripts along with 11 714 cancer breakpoints. In this latest version, we have included multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, RefSeq and the Mitelman collection for every entry in the ‘Full Collection’. In addition, for every chimera, we have added a predicted chimeric protein–protein interaction (ChiPPI) network , which allows for easy visualization of protein partners of both parental and fusion proteins for all human chimeras. The database contains a comprehensive annotation for 34 922 chimeric transcripts from eight organisms, and includes the manual annotation of 200 sense-antiSense (SaS) chimeras. The current improvements in the content and functionality to the ChiTaRS database make it a central resource for the study of chimeric transcripts and fusion proteins.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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