相关论文: Unbiased simulation of structural transitions in c…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…

The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…

We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…

Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…

The synthetic actin network demands great interest as bio-material due to its soft and wet nature that mimic many biological scaffolding structures. The study of these structures can contribute to a better understanding of this new…

The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local…

Machining time is a major performance criterion when it comes to high-speed machining. CAM software can help in estimating that time for a given strategy. But in practice, CAM-programmed feed rates are rarely achieved, especially where…

Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…

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…

We present an algorithm which is designed to allow the efficient identification and preliminary dynamical analysis of thousands of structures and substructures in large N-body simulations. First we utilise a refined density gradient system…

We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…

We present a general framework for the efficient simulation of realistic fermionic systems with modern machine learning inspired representations of quantum many-body states, towards a universal tool for ab initio electronic structure. These…

The interpretability of machine learning, particularly for deep neural networks, is crucial for decision making in real-world applications. One approach is replacing the un-interpretable machine learning model with a surrogate model, which…

To rigorously model fast ions in fusion plasmas, a non-Maxwellian equilibrium distribution must be used. In the work, the response of high-energy alpha particles to electrostatic turbulence has been analyzed for several different tokamak…

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…

A multiscale scheme combining molecular dynamics (MD) and microscopic phase-field theory is proposed to study the structural phase transformations in solids with inhomogeneous strain field. The approach calculates strain response based on…

We propose a generalized Langevin dynamics (GLD) technique to construct non-Markovian particle-based coarse-grained models from fine-grained reference simulations and to efficiently integrate them. The proposed GLD model has the form of a…

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…

We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…

The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…