Related papers: A Rational Approach to Ring Flexibility in Interna…
We employ molecular dynamics simulations to explore how internal flexibility affects phase transitions in soft-matter systems composed of dimers interacting via a core-softened potential with two characteristic length scales. Monomers are…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
This work presents new tools for studying reachability and set invariance for continuous-time mixed-monotone dynamical systems subject to a disturbance input. The vector field of a mixed-monotone system is decomposable via a decomposition…
Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the…
The dynamics of geometrically non-linear flexible filaments play an important role in a host of biological processes, from flagella-driven cell transport to the polymeric structure of complex fluids. Such problems have historically been…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
Dynamic treatment regimes are sequential decision rules that adapt treatment according to individual time-varying characteristics and outcomes to achieve optimal effects, with applications in precision medicine, personalized…
The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for untangled (i.e. non-concatenated and unknotted) rings,…
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic…
Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N=1600 monomers per chain which…
The extension of the highly-optimized local natural orbital (LNO) CCSD(T) method is presented for high-spin open-shell molecules. The techniques enabling the outstanding efficiency of the closed-shell LNO-CCSD(T) variant are adopted,…
Molecular machines described in this paper are meant to be such molecular systems that make use of conformational mobility (i.e. hindered rotation around chemical bonds and molecular construction deformations with formation and breakage of…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
This study investigates the probability of threading in star catenanes under good solvent conditions using molecular dynamics simulations, emphasizing the influence of ring rigidity. Threading in these systems arises from the interplay…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…