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1703 Publications visible to you, out of a total of 1703
Type Ia supernova progenitors: a contemporary view of a long-standing puzzle

Abstract

Not specified

Authors: Ashley Jade Ruiter, Ivo Rolf Seitenzahl

Date Published: 1st Dec 2025

Publication Type: Journal

Distanzbasierte Inferenz von Genbäumen unter Berücksichtigung ihres Speziesbaumes

Abstract (Expand)

In dieser Arbeit wird Spearfish, eine neue Methode zur distanzbasierten Inferenz von Genbäumen, entwickelt und getestet. Spearfish verwendet die paarweisen Distanzen der Gensequenzen, sowie die Distanzen … der zugehörigen Spezies im Speziesbaum, in einem Clustering-Verfahren, um 10 Genbäume zu rekonstruieren. Der beste wird anschließend mithilfe eines statistischen Evaluierungsverfahrens ausgewählt. Auf allen getesteten simulierten Datensätzen konnte gezeigt werden, dass die von Spearfish inferierten Bäume durchschnittlich eine Distanz von 0,213 zum echten Genbaum besitzen. Damit ist es 2,18-mal genauer als Methoden wie RAxML-NG, welche den Speziesbaum nicht berücksichtigen. Spearfish ist 25,85% ungenauer, aber 49,63% schneller als GeneRax, eine der führenden Methoden, die Genbäume mithilfe ihres Speziesbaumes korrigieren. So kann Spearfish verwendet werden, um Startbäume für GeneRax zu rekonstruieren oder bei goßen Datensätzen sogar zu ersetzen.

Authors: Lukas Knirsch, Benoit Morel, Alexandros Stamatakis

Date Published: 2nd Oct 2025

Publication Type: Bachelor's Thesis

On the determinants of electron transfer reorganization energy in a cytochrome P450: cytochrome b5 complex. A combined quantum mechanics and molecular dynamics simulation study

Abstract (Expand)

The electron transfer steps in the catalytic cycle of cytochrome P450 (CYP) enzymes, ubiquitous proteins with key roles in processes such as drug metabolism and steroidogenesis, are often rate-limiting. …rate-limiting. To predict ET rates from atomistic molecular dynamics simulations using Marcus theory, values of the reaction free energy ΔG0 and the reorganization free energy λ are required from either experiments or computations. For the reduction of cytochrome P450 17A1 (CYP17A1) by the secondary redox protein cytochrome b5 (CYb5), a critical step in the regulation of steroidogenesis, experimental measurements of λ are not available. We here describe the computation of λ for this system from a combination of molecular mechanics/molecular dynamics simulations and quantum mechanics computations. Our results show that a quantum mechanical treatment of the redox-active cofactors is necessary, even though the surrounding protein and solvent, which are modeled classically, contribute most to the reorganization energy. The values of λ computed for structural ensembles corresponding to two predicted binding modes of the proteins are 1.23 and 1.16 eV. We find that the λ values computed for the individual soluble globular domains of the two proteins sum to approximately the λ values computed for the membrane-bound CYP17A1-CYb5 complex, indicating that additivity can be invoked in a computationally efficient approach to estimating λ values for such protein–protein complexes.

Authors: J. Teuffel, G. Mukherjee, S. B. Han, M. Elstner, R. C. Wade

Date Published: 21st May 2025

Publication Type: Journal

Enhancing the statistical evaluation of earthquake forecasts—An application to Italy

Abstract

Not specified

Authors: Jonas R. Brehmer, Kristof Kraus, Tilmann Gneiting, Marcus Herrmann, Warner Marzocchi

Date Published: 1st May 2025

Publication Type: Journal

Journey to the center of the common envelope evolution

Abstract (Expand)

Three-dimensional hydrodynamical simulations of common envelope evolution are often terminated soon after the initial dynamical plunge of the companion transitions into a long-lasting post-dynamical … long-lasting post-dynamical inspiral with a slowly varying semimajor axis, a b . This premature termination is often due to insufficient numerical resolution and challenges associated with the softening of the gravitational potential of the two cores. In this work we used statically refined 3D hydrodynamical simulations to study non-accreting binaries orbiting inside a common envelope, exploring the effects of varying numerical resolution, δ , gravitational potential softening prescriptions, and the associated softening length scale, ϵ . We find that quantities such as the binary inspiral timescale or the volume-averaged shearing rate typically converge to asymptotic values only for ϵ ≤0.1 a b and δ ≤6×10 −3 a b , with smaller ϵ requiring correspondingly smaller δ . This suggests that many of the contemporary simulations could effectively be under-resolved. After a few tens of binary orbits, the two cores become surrounded by a corotating, nearly hydrostatic gas structure that resembles the shared envelope of a contact binary. We propose that this structure is responsible for the slowing of the dynamical inspiral, leading to an asymptotic inspiral timescale of approximately 10 5 orbital periods for a binary mass ratio q =1/3, and approximately 10 6 orbital periods for a binary mass ratio q =1. Even in the absence of magnetic fields, we observe intermittent polar outflows collimated by partially centrifugally evacuated polar funnels. We discuss the implications for the long-term evolution in the post-dynamical inspiral phase and the ultimate emergence of the post-common-envelope binary.

Authors: Damien Gagnier, Ondřej Pejcha

Date Published: 1st May 2025

Publication Type: Journal

Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms

Abstract

Not specified

Authors: Christina Athanasiou, Ainara Claveras Cabezudo, Alexandros Tsengenes, Rebecca C. Wade

Date Published: 27th Apr 2025

Publication Type: Journal

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

Abstract (Expand)

The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a …we introduce a complementarity-determining region (CDR) grafting approach for designing nanobodies (Nbs) that target specific epitopes, with the aid of computer simulation and machine learning. As a proof-of-concept, we designed, evaluated, and characterized a high-affinity Nb against the spike protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. The designed Nb, referred to as Nb Ab.2, was synthesized and displayed high-affinity for both the purified receptor-binding domain protein and to the virus-like particle, demonstrating affinities of 9 nM and 60 nM, respectively, as measured with microscale thermophoresis. Circular dichroism showed the designed protein’s structural integrity and its proper folding, whereas molecular dynamics simulations provided insights into the internal dynamics of Nb Ab.2. This study shows that our computational pipeline can be used to efficiently design high-affinity Nbs with diagnostic and prophylactic potential, which can be tailored to tackle different viral targets.

Authors: Matheus VF Ferraz, W Camilla S Adan, Tayná E Lima, Adriele JC Santos, Sérgio O de Paula, Rafael Dhalia, Gabriel L Wallau, Rebecca C Wade, Isabelle FT Viana, Roberto D Lins

Date Published: 21st Apr 2025

Publication Type: Journal

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