Related papers: Understanding three-body contributions to coarse-g…
Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…
A self-consistent many-body approach is proposed to build a first-principles crystal field theory, where crystal field parameters are calculated ab initio. Many-body theory is used to write the energy of the interacting system as a function…
We introduce a machine-learning-based coarse-grained molecular dynamics (CGMD) model that faithfully retains the many-body nature of the inter-molecular dissipative interactions. Unlike common empirical CG models, the present model is…
We derive four-dimensional relativistic three-body equations for the case of a field theory with a three-point interaction vertex. These equations describe the coupled 2->2, 2->3, and 3->3 processes, and provide the means of calculating the…
The present thesis aims at studying the properties of symmetric nuclear and pure neutron matter from a Green's functions point of view, including two-body and three-body chiral forces. An extended self-consistent Green's function formalism…
The techniques of data-driven backmapping from coarse-grained (CG) to fine-grained (FG) representation often struggle with accuracy, unstable training, and physical realism, especially when applied to complex systems such as proteins. In…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
An expression for the stress tensor near an external boundary of a discrete mechanical system is derived explicitly in terms of the constituents' degrees of freedom and interaction forces. Starting point is the exact and general coarse…
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent,…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Starting from the basic path integral in phase space we reconsider the functional approach to the RG flow of the one particle irreducible effective average action. On employing a balanced coarse-graining procedure for the canonical…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of…
We present a real-space formulation for coarse-graining Kohn-Sham Density Functional Theory that significantly speeds up the analysis of material defects without appreciable loss of accuracy. The approximation scheme consists of two steps.…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (DCM), and solvated K$^+$ and Cl$^-$ ions. For the electrostatics, point charges (PCs) and machine…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…
We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
Despite the intense activity at the electronic and atomistic resolutions, coarse grained (CG) modeling of MOFs remains largely unexplored. One of the main reasons for this is the lack of adequate CG force fields. In this work, we present…