Related papers: Protein simulations combining an all-atom force fi…
All-atom molecular simulations offer detailed insights into macromolecular phenomena, but their substantial computational cost hinders the exploration of complex biological processes. We introduce Advanced Machine-learning Atomic…
By combining different ideas, a general and efficient protocol to deal with discontinuous phase transitions at low temperatures is proposed. For small $T$'s, it is possible to derive a generic analytic expression for appropriate order…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
From the underlying Master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Parameterized artificial neural networks (ANNs) can be very expressive ansatzes for variational algorithms, reaching state-of-the-art energies on many quantum many-body Hamiltonians. Nevertheless, the training of the ANN can be slow and…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
Two important enhanced sampling algorithms, simulated (ST) and parallel (PT) tempering, are commonly used when ergodic simulations may be hard to achieve, e.g, due to a phase space separated by large free-energy barriers. This is so for…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
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…
The use of external restraints is ubiquitous in advanced molecular simulation techniques. In general, restraints serve to reduce the configurational space that is available for sampling, thereby reducing the computational demands associated…
Increasing complexity in the power system and the transformation towards a smart grid lead to the necessity of new tools and methods for the development and testing of new technologies. One testing method is co-simulation, which allows…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…