An extrapolation method for the efficient calculation of molecular response properties within Born-Oppenheimer molecular dynamics

The calculation of molecular response properties in dynamic molecular systems is a major challenge that requires sampling over many steps of, e. g., Born-Oppenheimer molecular dynamics (BO-MD) simulations. We present an extrapolation scheme to accelerate such calculations for multiple steps within BO-MD trajectories or equivalently within other sampling methods of conformational space. The extrapolation scheme is related to the one introduced by Pulay and Fogarasi Chem. Phys. Lett., 2004, 386, 272] for self-consistent field (SCF) energy calculations. We extend the extrapolation to the quantities within our density matrix-based Laplace-transformed coupled perturbed SCF (DL-CPSCF) method that allows for linear-scaling calculations of response properties for large molecular systems. Here, we focus on the example of calculating NMR chemical shifts for which the number of required DL-CPSCF iterations reduces by roughly 40-70%

Hydrodynamic and Non-hydrodynamic Excitations in Kinetic Theory -- A Numerical Analysis in Scalar Field Theory

Viscous hydrodynamics serves as a successful mesoscopic description of the Quark-Gluon Plasma produced in relativistic heavy-ion collisions. In order to investigate, how such an effective description emerges from the underlying microscopic dynamics we calculate the hydrodynamic and non-hydrodynamic modes of linear response in the sound channel from a first-principle calculation in kinetic theory. We do this with a new approach wherein we discretize the collision kernel to directly calculate eigenvalues and eigenmodes of the evolution operator. This allows us to study the Green's functions at any point in the complex frequency space. Our study focuses on scalar theory with quartic interaction and we find that the analytic structure of Green's functions in the complex plane is far more complicated than just poles or cuts which is a first step towards an equivalent study in QCD kinetic theory.Comment: 30 pages and 8 figures. v2 changes: Added a more nuanced discussion about hydrodynamization in introduction. Clarified the potential differences between the QFT scalar \phi^4 theory and kinetic theory derived from it. Added some additional discussion of a hydrodynamic breakdown scale k_c to the conclusion of the paper. Fixed some typo

Universality of sound modes in kinetic theory

We present a simple approach to extract hydrodynamic sound modes and non-hydrodynamic modes in kinetic theories from response functions of the energy-momentum tensor. By comparing the response functions in four types of kinetic theories, namely the Relaxation-Time Approximation, scalar $\phi^4$ theory, SU(3) Yang-Mills theory and QCD kinetic theory, we find a remarkable degree of universality for the sound mode, even beyond the hydrodynamic regime.Comment: 6 pages, 4 figures; Proceeding on 11th International Conference on Hard and Electromagnetic Probes of High Energy Nuclear Collisions (Hard Probe 2023), 26-31 March 2023, Aschaffenburg, German

A Base-Independent Repair Mechanism for DNA Glycosylase-No Discrimination Within the Active Site

The ubiquitous occurrence of DNA damages renders its repair machinery a crucial requirement for the genomic stability and the survival of living organisms. Deficiencies in DNA repair can lead to carcinogenesis, Alzheimer, or Diabetes II, where increased amounts of oxidized DNA bases have been found in patients. Despite the highest mutation frequency among oxidized DNA bases, the base-excision repair process of oxidized and ring-opened guanine, FapydG (2, 6-diamino-4-hydroxy-5-formamidopyrimidine),remained unclear since it is difficult to study experimentally. We use newly-developed linear-scaling quantum-chemical methods (QM) allowing us to include up to 700 QM-atoms and achieving size convergence. Instead of the widely assumed base-protonated pathway we find a ribose-protonated repair mechanism which explains experimental observations and shows strong evidence for a base-independent repair process. Our results also imply that discrimination must occur during recognition, prior to the binding within the active site

The gender income gap and the influence of family formation reconsidered

In her recent study Bobbitt-Zeher (2007) takes on the important task of identifying the contribution of educational factors relative to non-educational factors in the making of the gender income gap among the college-educated and finds that “family formation has virtually no effect on the income gap” (Ibid.:13). In this methodological comment we argue that she was led to this conclusion prematurely because her analysis falls short in several respects. We explicate the problems, delineate alternatives and replicate her analysis with similar German data. We find that each of the shortcomings leads to negative bias concerning the influence of family formation. Our results show that family formation is likely to be the single most important factor in the explanation of the income gap

The gender income gap and the influence of family formation reconsidered

In her recent study Bobbitt-Zeher (2007) takes on the important task of identifying the contribution of educational factors relative to non-educational factors in the making of the gender income gap among the college-educated and finds that “family formation has virtually no effect on the income gap” (Ibid.:13). In this methodological comment we argue that she was led to this conclusion prematurely because her analysis falls short in several respects. We explicate the problems, delineate alternatives and replicate her analysis with similar German data. We find that each of the shortcomings leads to negative bias concerning the influence of family formation. Our results show that family formation is likely to be the single most important factor in the explanation of the income gap