Related papers: Protein simulations combining an all-atom force fi…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…
We propose a new field-level emulator that bridges two simulators using unpaired simulation datasets. Our method leverages a flow-based approach to learn the likelihood transport from one simulator to the other. Since multiple transport…
Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape…
We demonstrate that Dirac fermions self-interacting or coupled to dynamic scalar fields can emerge in the low energy sector of designed bosonic and fermionic cold atom systems. We illustrate this with two examples defined in two spacetime…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic…
In the dynamic field of materials science, the quest to find optimal structures with low potential energy is of great significance. Over the past two decades, the minima hopping algorithm has emerged as a successful tool in this pursuit. We…
The parallel-tempering method has been applied to numerically study the thermodynamic behavior of a three-dimensional disordered antiferromagnetic Ising model with random fields at spin concentrations corresponding to regions of both weak…
The paper provides a tutorial to the conceptual layout of a self-consistently coupled Particle-In-Cell/Test-Particle model for the kinetic simulation of sputtering transport in capacitively coupled plasmas at low gas pressures. It explains…
The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods are often grouped into two broad families. On the one hand…
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…
Parallel tempering, also known as replica exchange sampling, is an important method for simulating complex systems. In this algorithm simulations are conducted in parallel at a series of temperatures, and the key feature of the algorithm is…
An effective model for the spacetime foam is constructed in terms of nonlocal interactions in a classical background. In the weak-coupling approximation, the evolution of the low-energy density matrix is determined by a master equation that…
Granular materials are heterogenous grains in contact, which are ubiquitous in many scientific and engineering applications such as chemical engineering, fluid mechanics, geomechanics, pharmaceutics, and so on. Granular materials pose a…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…