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Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
We describe the adaptive resolution multiscale method AdResS. The conceptual evolution as well as the improvements of its technical efficiency are described step by step, with an explicit reference to current limitations and open problems.
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…
Quantum geometrical molecular dynamics provides a quantum geometric picture for understanding reactive dynamics, especially excited-state conical intersection dynamics, and also a numerically exact method for strongly correlated…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to…
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…