Related papers: Enhanced sampling methods for molecular dynamics s…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
Simulation studies are widely used to evaluate statistical methods. However, new methods are often introduced and evaluated using data-generating mechanisms (DGMs) devised by the same authors. This coupling creates misaligned incentives,…
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…
Quantum computing has the potential to revolutionize multiple fields by solving complex problems that can not be solved in reasonable time with current classical computers. Nevertheless, the development of quantum computers is still in its…
This paper discusses new simulation algorithms for stochastic chemical kinetics that exploit the linearity of the chemical master equation and its matrix exponential exact solution. These algorithms make use of various approximations of the…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in…
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…
Hard spheres are arguably one of the most fundamental model systems in soft matter physics, and hence a common topic of simulation studies. Event-driven simulation methods provide an efficient method for studying the phase behavior and…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
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…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
Optimization algorithms and Monte Carlo sampling algorithms have provided the computational foundations for the rapid growth in applications of statistical machine learning in recent years. There is, however, limited theoretical…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We describe an improved version of the quantum simulation method based on the implementation of a truncated Taylor series of the evolution operator. The idea is to add an extra step to the previously known algorithm which implements an…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting…
The search for new, application-specific quantum computers designed to outperform any classical computer is driven by the ending of Moore's law and the quantum advantages potentially obtainable. Photonic networks are promising examples,…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Recent advancements in robotics have transformed industries such as manufacturing, logistics, surgery, and planetary exploration. A key challenge is developing efficient motion planning algorithms that allow robots to navigate complex…