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The steady state velocity fluctuations of a movable piston located on the top of a vibrated granular gas are studied by means of molecular dynamics simulations. From the second moment of the distribution, a temperature parameter for the…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed, but,…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
A numerical model able to simulate solid-state constrained sintering is presented. The model couples an existing kinetic Monte Carlo (kMC) model for free sintering with a finite element model (FEM) for calculating stresses on a…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
Magnetic gels are soft elastic materials consisting of magnetic particles embedded in a polymer network. Their shape and elasticity can be controlled by an external magnetic field, which gives rise to both, engineering and biomedical…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
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…
Indentation tests are classical tools to determine material properties. For biological samples such as cysts of cells, however, the observed force-displacement relation cannot be expected to follow predictions for simple materials. Here, by…
Model compression has been introduced to reduce the required hardware resources while maintaining the model accuracy. Lots of techniques for model compression, such as pruning, quantization, and low-rank approximation, have been suggested…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
We apply adaptive feedback for the partial refrigeration of a mechanical resonator, i.e. with the aim to simultaneously cool the classical thermal motion of more than one vibrational degree of freedom. The feedback is obtained from a neural…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…