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A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. Moreover, they are increasingly used in combination with traction force microscopy on soft…
This paper presents an extended coarse-grained investigation of the elastic properties of polystyrene. In particular, we employ the well-known MARTINI force field and its modifications to perform extended molecular dynamics simulations at…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Accurately predicting protein melting temperature changes (Delta Tm) is fundamental for assessing protein stability and guiding protein engineering. Leveraging multi-modal protein representations has shown great promise in capturing the…
Continual Learning with Pre-trained Models holds great promise for efficient adaptation across sequential tasks. However, most existing approaches freeze PTMs and rely on auxiliary modules like prompts or adapters, limiting model plasticity…
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…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the…
Foundational Machine Learning Potentials can resolve the accuracy and transferability limitations of classical force fields. They enable microscopic insights into material behavior through Molecular Dynamics simulations, which can crucially…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Using the perturbation-response scanning (PRS) technique, we study a set of 23 proteins that display a variety of conformational motions upon ligand binding (e.g. shear, hinge, allosteric). In most cases, PRS determines residues that may be…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
We consider an immersed elastic body that is actively driven through a structured fluid by a motor or an external force. The behavior of such a system generally cannot be solved analytically, necessitating the use of numerical methods.…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
Frictional properties of interfaces with dynamic chemical bonds have been the subject of intensive experimental investigation and modeling, as it provides important insights into the molecular origin of the empirical rate and state laws,…