Grubmüller, Helmut

[["dc.bibliographiccitation.artnumber","1709"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-05-02T08:02:06Z"],["dc.date.available","2022-05-02T08:02:06Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft"],["dc.identifier.doi","10.1038/s41467-022-29332-2"],["dc.identifier.pii","29332"],["dc.identifier.pmid","35361752"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/107232"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/503"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-561"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","2041-1723"],["dc.relation.workinggroup","RG Grubmüller"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Effects of cryo-EM cooling on structural ensembles"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2258"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","2269"],["dc.bibliographiccitation.volume","50"],["dc.contributor.author","Kolář, Michal H."],["dc.contributor.author","Nagy, Gabor"],["dc.contributor.author","Kunkel, John"],["dc.contributor.author","Vaiana, Sara M."],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-04-01T10:02:53Z"],["dc.date.available","2022-04-01T10:02:53Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest."],["dc.identifier.doi","10.1093/nar/gkac038"],["dc.identifier.pmid","35150281"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/106030"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/502"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.relation.workinggroup","RG Grubmüller"],["dc.rights","CC BY 4.0"],["dc.title","Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e38302"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","PLoS ONE"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Risselada, Herre Jelger"],["dc.contributor.author","Marelli, Giovanni"],["dc.contributor.author","Fuhrmans, Marc"],["dc.contributor.author","Smirnova, Yuliya G."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Marrink, Siewert Jan"],["dc.contributor.author","Mueller, Marcus"],["dc.date.accessioned","2017-09-07T11:48:51Z"],["dc.date.available","2017-09-07T11:48:51Z"],["dc.date.issued","2012"],["dc.description.abstract","Our molecular simulations reveal that wild-type influenza fusion peptides are able to stabilize a highly fusogenic pre-fusion structure, i.e. a peptide bundle formed by four or more trans-membrane arranged fusion peptides. We rationalize that the lipid rim around such bundle has a non-vanishing rim energy (line-tension), which is essential to (i) stabilize the initial contact point between the fusing bilayers, i. e. the stalk, and (ii) drive its subsequent evolution. Such line-tension controlled fusion event does not proceed along the hypothesized standard stalk-hemifusion pathway. In modeled influenza fusion, single point mutations in the influenza fusion peptide either completely inhibit fusion (mutants G1V and W14A) or, intriguingly, specifically arrest fusion at a hemifusion state (mutant G1S). Our simulations demonstrate that, within a line-tension controlled fusion mechanism, these known point mutations either completely inhibit fusion by impairing the peptide's ability to stabilize the required peptide bundle (G1V and W14A) or stabilize a persistent bundle that leads to a kinetically trapped hemifusion state (G1S). In addition, our results further suggest that the recently discovered leaky fusion mutant G13A, which is known to facilitate a pronounced leakage of the target membrane prior to lipid mixing, reduces the membrane integrity by forming a 'super' bundle. Our simulations offer a new interpretation for a number of experimentally observed features of the fusion reaction mediated by the prototypical fusion protein, influenza hemagglutinin, and might bring new insights into mechanisms of other viral fusion reactions."],["dc.identifier.doi","10.1371/journal.pone.0038302"],["dc.identifier.fs","587227"],["dc.identifier.gro","3142512"],["dc.identifier.isi","000305826400002"],["dc.identifier.pmid","22761674"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/7878"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/8871"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1932-6203"],["dc.relation.orgunit","Fakultät für Physik"],["dc.rights","CC BY 2.5"],["dc.rights.uri","http://creativecommons.org/licenses/by/2.5/"],["dc.title","Line-Tension Controlled Mechanism for Influenza Fusion"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","139"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","155"],["dc.bibliographiccitation.volume","41"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Lange, Oliver F."],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Brueschweiler, Rafael"],["dc.contributor.author","Munk, Axel"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:48:16Z"],["dc.date.available","2017-09-07T11:48:16Z"],["dc.date.issued","2008"],["dc.description.abstract","Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of internuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 mu s). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters independent of the details of the structure used for alignment tensor calculation-as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors < S-rdc(2)> = 0: 72 +/- 0: 02 compared to < S-LS(2)> = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S-rdc(2) (NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-tau(c) time scale (S-rdc(2) (NH) = 0.59 +/- 0.03), while it is inconspicuous (S-LS(2) (NH) = 0.82) on the sub-tau(c) as well as on mu s-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data."],["dc.identifier.doi","10.1007/s10858-008-9244-4"],["dc.identifier.gro","3143271"],["dc.identifier.isi","000257224700004"],["dc.identifier.pmid","18523727"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11216"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/766"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: NIGMS NIH HHS [GM 066041, R01 GM066041]"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0925-2738"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","581"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","589"],["dc.bibliographiccitation.volume","97"],["dc.contributor.author","Goette, Maik"],["dc.contributor.author","Stumpe, Martin C."],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:46:52Z"],["dc.date.available","2017-09-07T11:46:52Z"],["dc.date.issued","2009"],["dc.description.abstract","The transport of large biomolecules such as proteins and RNA across nuclear pore complexes is afield of strong interest and research. Although the basic mechanisms are fairly well understood, the details of the underlying intermolecular interaction within these transport complexes are still unclear. The recognition dynamics and energetics of cargo binding to the transport receptor are not yet resolved. Here, the binding of dimethylated RNA-caps to snurportin 1 is studied by molecular-dynamics simulations. The simulations reveal a strong structural response of the protein upon RNA-cap release. In particular, major rearrangements occur in regions already intrinsically flexible in the holo structure. Additionally, the difference in free energy of binding to snurportin 1 between the two methylation states of the RNA-cap, responsible for the directionality of the transport is quantified. In particular, desolvation of the ligand is revealed as the key-step in binding to snurportin 1. These findings suggest that the binding of m(3)G-capped RNA is mainly driven by the enhanced water entropy gain of the solvation shell."],["dc.identifier.doi","10.1016/j.bpj.2009.04.049"],["dc.identifier.gro","3143084"],["dc.identifier.isi","000268428700020"],["dc.identifier.pmid","19619473"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11288"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/559"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0006-3495"],["dc.rights","CC BY-NC-ND 3.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc-nd/3.0"],["dc.title","Molecular Determinants of Snurportin 1 Ligand Affinity and Structural Response upon Binding"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4466"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Beckert, Bertrand"],["dc.contributor.author","Leroy, Elodie C."],["dc.contributor.author","Sothiselvam, Shanmugapriya"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Svetlov, Maxim S."],["dc.contributor.author","Graf, Michael"],["dc.contributor.author","Arenz, Stefan"],["dc.contributor.author","Abdelshahid, Maha"],["dc.contributor.author","Seip, Britta"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Mankin, Alexander S."],["dc.contributor.author","Innis, C. Axel"],["dc.contributor.author","Vázquez-Laslop, Nora"],["dc.contributor.author","Wilson, Daniel N."],["dc.date.accessioned","2022-02-22T15:58:02Z"],["dc.date.available","2022-02-22T15:58:02Z"],["dc.date.issued","2021"],["dc.description.abstract","Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics."],["dc.identifier.doi","10.1038/s41467-021-24674-9"],["dc.identifier.pmid","34294725"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/100197"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/415"],["dc.language.iso","en"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.issn","2041-1723"],["dc.relation.orgunit","Max-Planck-Institut für biophysikalische Chemie"],["dc.relation.workinggroup","RG Grubmüller"],["dc.rights","CC BY 4.0"],["dc.title","Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","5984"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Milovanovic, Dragomir"],["dc.contributor.author","Honigmann, Alf"],["dc.contributor.author","Koike, Seiichi"],["dc.contributor.author","Göttfert, Fabian"],["dc.contributor.author","Pähler, Gesa"],["dc.contributor.author","Junius, Meike"],["dc.contributor.author","Müllar, Stefan"],["dc.contributor.author","Diederichsen, Ulf"],["dc.contributor.author","Janshoff, Andreas"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Risselada, H. J."],["dc.contributor.author","Eggeling, Christian"],["dc.contributor.author","Hell, Stefan"],["dc.contributor.author","van den Bogaart, Geert"],["dc.contributor.author","Jahn, Reinhard"],["dc.date.accessioned","2017-09-07T11:44:46Z"],["dc.date.available","2017-09-07T11:44:46Z"],["dc.date.issued","2015"],["dc.description.abstract","The clustering of proteins and lipids in distinct microdomains is emerging as an important principle for the spatial patterning of biological membranes. Such domain formation can be the result of hydrophobic and ionic interactions with membrane lipids as well as of specific protein-protein interactions. Here using plasma membrane-resident SNARE proteins as model, we show that hydrophobic mismatch between the length of transmembrane domains (TMDs) and the thickness of the lipid membrane suffices to induce clustering of proteins. Even when the TMDs differ in length by only a single residue, hydrophobic mismatch can segregate structurally closely homologous membrane proteins in distinct membrane domains. Domain formation is further fine-tuned by interactions with polyanionic phosphoinositides and homo and heterotypic protein interactions. Our findings demonstrate that hydrophobic mismatch contributes to the structural organization of membranes."],["dc.identifier.doi","10.1038/ncomms6984"],["dc.identifier.fs","613597"],["dc.identifier.gro","3141986"],["dc.identifier.isi","000348812100002"],["dc.identifier.pmid","25635869"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13586"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3279"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","2041-1723"],["dc.rights.access","openAccess"],["dc.subject.mesh","Animals"],["dc.subject.mesh","Fluorescence Resonance Energy Transfer"],["dc.subject.mesh","Fluorescent Antibody Technique"],["dc.subject.mesh","Humans"],["dc.subject.mesh","Hydrophobic and Hydrophilic Interactions"],["dc.subject.mesh","Molecular Dynamics Simulation"],["dc.subject.mesh","Phosphatidylinositols"],["dc.subject.mesh","Protein Binding"],["dc.subject.mesh","Protein Structure, Tertiary"],["dc.subject.mesh","Rats"],["dc.subject.mesh","SNARE Proteins"],["dc.title","Hydrophobic mismatch sorts SNARE proteins into distinct membrane domains"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5766"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Journal of chemical theory and computation"],["dc.bibliographiccitation.lastpage","5776"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Schultze, Steffen"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-11-17T18:39:23Z"],["dc.date.available","2021-11-17T18:39:23Z"],["dc.date.issued","2021-09-14"],["dc.description.abstract","Time-lagged independent component analysis (tICA) is a widely used dimension reduction method for the analysis of molecular dynamics (MD) trajectories and has proven particularly useful for the construction of protein dynamics Markov models. It identifies those \"slow\" collective degrees of freedom onto which the projections of a given trajectory show maximal autocorrelation for a given lag time. Here we ask how much information on the actual protein dynamics and, in particular, the free energy landscape that governs these dynamics the tICA-projections of MD-trajectories contain, as opposed to noise due to the inherently stochastic nature of each trajectory. To answer this question, we have analyzed the tICA-projections of high dimensional random walks using a combination of analytical and numerical methods. We find that the projections resemble cosine functions and strongly depend on the lag time, exhibiting strikingly complex behavior. In particular, and contrary to previous studies of principal component projections, the projections change noncontinuously with increasing lag time. The tICA-projections of selected 1 μs protein trajectories and those of random walks are strikingly similar, particularly for larger proteins, suggesting that these trajectories contain only little information on the energy landscape that governs the actual protein dynamics. Further the tICA-projections of random walks show clusters very similar to those observed for the protein trajectories, suggesting that clusters in the tICA-projections of protein trajectories do not necessarily reflect local minima in the free energy landscape. We also conclude that, in addition to the previous finding that certain ensemble properties of nonconverged protein trajectories resemble those of random walks; this is also true for their time correlations."],["dc.identifier.doi","10.1021/acs.jctc.1c00273"],["dc.identifier.pmid","34449229"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/93175"],["dc.language.iso","en"],["dc.relation","SFB 1456: Mathematik des Experiments: Die Herausforderung indirekter Messungen in den Naturwissenschaften"],["dc.relation","SFB 1456 | Cluster C: Data with Information in Their Dependency Structure"],["dc.relation","SFB 1456 | Cluster C | C02: Stochastic computed tomography: theory and algorithms for single-shot X-FEL imaging"],["dc.relation.eissn","1549-9626"],["dc.relation.issn","1549-9618"],["dc.relation.issn","1549-9626"],["dc.relation.orgunit","Max-Planck-Institut für biophysikalische Chemie"],["dc.rights","CC BY 4.0"],["dc.title","Time-Lagged Independent Component Analysis of Random Walks and Protein Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","97"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","The International Journal of High Performance Computing Applications"],["dc.bibliographiccitation.lastpage","117"],["dc.bibliographiccitation.volume","35"],["dc.contributor.author","Kohnke, Bartosz"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Beckmann, Andreas"],["dc.contributor.author","Lube, Gert"],["dc.contributor.author","Kabadshow, Ivo"],["dc.contributor.author","Dachsel, Holger"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:59:04Z"],["dc.date.available","2021-03-05T08:59:04Z"],["dc.date.issued","2021-01"],["dc.description.abstract","Solving an N-body problem, electrostatic or gravitational, is a crucial task and the main computational bottleneck in many scientific applications. Its direct solution is an ubiquitous showcase example for the compute power of graphics processing units (GPUs). However, the naïve pairwise summation has O ( N 2 ) computational complexity. The fast multipole method (FMM) can reduce runtime and complexity to O ( N ) for any specified precision. Here, we present a CUDA-accelerated, C++ FMM implementation for multi particle systems with r − 1 potential that are found, e.g. in biomolecular simulations. The algorithm involves several operators to exchange information in an octree data structure. We focus on the Multipole-to-Local (M2L) operator, as its runtime is limiting for the overall performance. We propose, implement and benchmark three different M2L parallelization approaches. Approach (1) utilizes Unified Memory to minimize programming and porting efforts. It achieves decent speedups for only little implementation work. Approach (2) employs CUDA Dynamic Parallelism to significantly improve performance for high approximation accuracies. The presorted list-based approach (3) fits periodic boundary conditions particularly well. It exploits FMM operator symmetries to minimize both memory access and the number of complex multiplications. The result is a compute-bound implementation, i.e. performance is limited by arithmetic operations rather than by memory accesses. The complete CUDA parallelized FMM is incorporated within the GROMACS molecular dynamics package as an alternative Coulomb solver."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft \t https://doi.org/10.13039/501100001659"],["dc.identifier.doi","10.1177/1094342020964857"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80346"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.publisher","SAGE Publications"],["dc.relation.eissn","1741-2846"],["dc.relation.issn","1094-3420"],["dc.rights","https://creativecommons.org/licenses/by/4.0/"],["dc.title","A CUDA fast multipole method with highly efficient M2L far field evaluation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","343001"],["dc.bibliographiccitation.issue","34"],["dc.bibliographiccitation.journal","Journal of Physics. D, Applied Physics"],["dc.bibliographiccitation.volume","51"],["dc.contributor.affiliation","Bassereau, Patricia;"],["dc.contributor.affiliation","Jin, Rui;"],["dc.contributor.affiliation","Baumgart, Tobias;"],["dc.contributor.affiliation","Deserno, Markus;"],["dc.contributor.affiliation","Dimova, Rumiana;"],["dc.contributor.affiliation","Frolov, Vadim A;"],["dc.contributor.affiliation","Bashkirov, Pavel V;"],["dc.contributor.affiliation","Grubmüller, Helmut;"],["dc.contributor.affiliation","Jahn, Reinhard;"],["dc.contributor.affiliation","Risselada, H Jelger;"],["dc.contributor.affiliation","Johannes, Ludger;"],["dc.contributor.affiliation","Kozlov, Michael M;"],["dc.contributor.affiliation","Lipowsky, Reinhard;"],["dc.contributor.affiliation","Pucadyil, Thomas J;"],["dc.contributor.affiliation","Zeno, Wade F;"],["dc.contributor.affiliation","Stachowiak, Jeanne C;"],["dc.contributor.affiliation","Stamou, Dimitrios;"],["dc.contributor.affiliation","Breuer, Artù;"],["dc.contributor.affiliation","Lauritsen, Line;"],["dc.contributor.affiliation","Simon, Camille;"],["dc.contributor.affiliation","Sykes, Cécile;"],["dc.contributor.affiliation","Voth, Gregory A;"],["dc.contributor.affiliation","Weikl, Thomas R;"],["dc.contributor.author","Bassereau, Patricia"],["dc.contributor.author","Jin, Rui"],["dc.contributor.author","Baumgart, Tobias"],["dc.contributor.author","Deserno, Markus"],["dc.contributor.author","Dimova, Rumiana"],["dc.contributor.author","Frolov, Vadim A"],["dc.contributor.author","Bashkirov, Pavel V"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Jahn, Reinhard"],["dc.contributor.author","Risselada, H. Jelger"],["dc.contributor.author","Johannes, Ludger"],["dc.contributor.author","Kozlov, Michael M."],["dc.contributor.author","Lipowsky, Reinhard"],["dc.contributor.author","Pucadyil, Thomas J."],["dc.contributor.author","Zeno, Wade F."],["dc.contributor.author","Stachowiak, Jeanne C."],["dc.contributor.author","Stamou, Dimitrios"],["dc.contributor.author","Breuer, Artù"],["dc.contributor.author","Lauritsen, Line"],["dc.contributor.author","Simon, Camille"],["dc.contributor.author","Sykes, Cécile"],["dc.contributor.author","Voth, Gregory A."],["dc.contributor.author","Weikl, Thomas R."],["dc.date.accessioned","2020-12-10T18:15:41Z"],["dc.date.available","2020-12-10T18:15:41Z"],["dc.date.issued","2018"],["dc.date.updated","2022-02-09T13:18:50Z"],["dc.description.abstract","Abstract The importance of curvature as a structural feature of biological membranes has been recognized for many years and has fascinated scientists from a wide range of different backgrounds. On the one hand, changes in membrane morphology are involved in a plethora of phenomena involving the plasma membrane of eukaryotic cells, including endo- and exocytosis, phagocytosis and filopodia formation. On the other hand, a multitude of intracellular processes at the level of organelles rely on generation, modulation, and maintenance of membrane curvature to maintain the organelle shape and functionality. The contribution of biophysicists and biologists is essential for shedding light on the mechanistic understanding and quantification of these processes. Given the vast complexity of phenomena and mechanisms involved in the coupling between membrane shape and function, it is not always clear in what direction to advance to eventually arrive at an exhaustive understanding of this important research area. The 2018 Biomembrane Curvature and Remodeling Roadmap of Journal of Physics D: Applied Physics addresses this need for clarity and is intended to provide guidance both for students who have just entered the field as well as established scientists who would like to improve their orientation within this fascinating area."],["dc.identifier.doi","10.1088/1361-6463/aacb98"],["dc.identifier.eissn","1361-6463"],["dc.identifier.issn","0022-3727"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/74924"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.publisher","IOP Publishing"],["dc.rights.uri","http://creativecommons.org/licenses/by/3.0/"],["dc.title","The 2018 biomembrane curvature and remodeling roadmap"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]