| 1. |
- Andersen, Jeppe R., et al.
(författare)
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A Positive Resampler for Monte Carlo events with negative weights
- 2020
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 80:11
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Tidskriftsartikel (refereegranskat)abstract
- We propose the Positive Resampler to solve the problem associated with event samples from state-of-the-art predictions for scattering processes at hadron colliders typically involving a sizeable number of events contributing with negative weight. The proposed method guarantees positive weights for all physical distributions, and a correct description of all observables. A desirable side product of the method is the possibility to reduce the size of event samples produced by General Purpose Event Generators, thus lowering the resource demands for subsequent computing-intensive event processing steps. We demonstrate the viability and efficiency of our approach by considering its application to a next-to-leading order + parton shower merged prediction for the production of a W boson in association with multiple jets.
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| 2. |
- Bothmann, Enrico, et al.
(författare)
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A standard convention for particle-level Monte Carlo event-variation weights
- 2023
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Ingår i: SciPost Physics Core. - 2666-9366. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Streams of event weights in particle-level Monte Carlo event generators are a convenient and immensely CPU-efficient approach to express systematic uncertainties in phenomenology calculations, providing systematic variations on the nominal prediction within a single event sample. But the lack of a common standard for labelling these variation streams across different tools has proven to be a major limitation for event-processing tools and analysers alike. Here we propose a well-defined, extensible community standard for the naming, ordering, and interpretation of weight streams that will serve as the basis for semantically correct parsing and combination of such variations in both theoretical and experimental studies.
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| 3. |
- Gavrilov, Yulian, et al.
(författare)
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Slow conformational changes in the rigid and highly stable chymotrypsin inhibitor 2
- 2023
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Ingår i: Protein Science. - : Wiley. - 0961-8368 .- 1469-896X. ; 32:4
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Tidskriftsartikel (refereegranskat)abstract
- Slow conformational changes are often directly linked to protein function. It is however less clear how such processes may perturb the overall folding stability of a protein. We previously found that the stabilizing double mutant L49I/I57V in the small protein chymotrypsin inhibitor 2 from barley led to distributed increased nanosecond and faster dynamics. Here we asked what effects the L49I and I57V substitutions, either individually or together, have on the slow conformational dynamics of CI2. We used 15N CPMG spin relaxation dispersion experiments to measure the kinetics, thermodynamics, and structural changes associated with slow conformational change in CI2. These changes result in an excited state that is populated to 4.3% at 1°C. As the temperature is increased the population of the excited state decreases. Structural changes in the excited state are associated with residues that interact with water molecules that have well defined positions and are found at these positions in all crystal structures of CI2. The substitutions in CI2 have only little effect on the structure of the excited state whereas the stability of the excited state to some extent follows the stability of the main state. The minor state is thus most populated for the most stable CI2 variant and least populated for the least stable variant. We hypothesize that the interactions between the substituted residues and the well-ordered water molecules links subtle structural changes around the substituted residues to the region in the protein that experience slow conformational changes.
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| 4. |
- Hendus-Altenburger, Ruth, et al.
(författare)
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The intracellular lipid-binding domain of human Na+/H+ exchanger 1 forms a lipid-protein co-structure essential for activity
- 2020
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic interactions of proteins with lipid membranes are essential regulatory events in biology, but remain rudimentarily understood and particularly overlooked in membrane proteins. The ubiquitously expressed membrane protein Na+/H+-exchanger 1 (NHE1) regulates intracellular pH (pHi) with dysregulation linked to e.g. cancer and cardiovascular diseases. NHE1 has a long, regulatory cytosolic domain carrying a membrane-proximal region described as a lipid-interacting domain (LID), yet, the LID structure and underlying molecular mechanisms are unknown. Here we decompose these, combining structural and biophysical methods, molecular dynamics simulations, cellular biotinylation- and immunofluorescence analysis and exchanger activity assays. We find that the NHE1-LID is intrinsically disordered and, in presence of membrane mimetics, forms a helical αα-hairpin co-structure with the membrane, anchoring the regulatory domain vis-a-vis the transport domain. This co-structure is fundamental for NHE1 activity, as its disintegration reduced steady-state pHi and the rate of pHi recovery after acid loading. We propose that regulatory lipid-protein co-structures may play equally important roles in other membrane proteins.
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