Publication Server of Zuse Institute Berlin (ZIB)
Not a member yet
6648 research outputs found
Sort by
Navigating protein landscapes with a machine-learned transferable coarse-grained model
No full textThe most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combining recent deep learning methods with a large and diverse training set of all-atom protein simulations, we here develop a bottom-up CG force field with chemical transferability, which can be used for extrapolative molecular dynamics on new sequences not used during model parametrization. We demonstrate that the model successfully predicts folded structures, intermediates, metastable folded and unfolded basins, and the fluctuations of intrinsically disordered proteins while it is several orders of magnitude faster than an all-atom model. This showcases the feasibility of a universal and computationally efficient machine-learned CG model for proteins
On the state of QUBO solving
No full textIt is regularly claimed that quantum computers will bring breakthrough progress in solving challenging combinatorial
optimization problems relevant in practice. In particular, Quadratic Unconstrained Binary Optimization
(QUBO) problems are said to be the model of choice for use in (adiabatic) quantum systems during the noisy intermediate-
scale quantum (NISQ) era. Even the first commercial quantum-based systems are advertised to solve
such problems. Theoretically, any Integer Program can be converted into a QUBO. In practice, however, there are
some caveats, as even for problems that can be nicely modeled as a QUBO, this might not be the most effective
way to solve them. We review the state of QUBO solving on digital and quantum computers and provide insights
regarding current benchmark instances and modeling
Approximating particle-based clustering dynamics by stochastic PDEs
No full textThis work proposes stochastic partial differential equations (SPDEs) as a practical tool to replicate clustering effects of more detailed particle-based dynamics. Inspired by membrane mediated receptor dynamics on cell surfaces, we formulate a stochastic particle-based model for diffusion and pairwise interaction of particles, leading to intriguing clustering phenomena. Employing numerical simulation and cluster detection methods, we explore the approximation of the particle-based clustering dynamics through mean-field approaches. We find that SPDEs successfully reproduce spatiotemporal clustering dynamics, not only in the initial cluster formation period, but also on longer time scales where the successive merging of clusters cannot be tracked by deterministic mean-field models. The computational efficiency of the SPDE approach allows us to generate extensive statistical data for parameter estimation in a simpler model that uses a Markov jump process to capture the temporal evolution of the cluster number
Clustering Time-Evolving Networks Using the Spatiotemporal Graph Laplacian
No full textTime-evolving graphs arise frequently when modeling complex dynamical systems such as social networks, traffic flow, and biological processes. Developing techniques to identify and analyze communities in these time-varying graph structures is an important challenge. In this work, we generalize existing spectral clustering algorithms from static to dynamic graphs using canonical correlation analysis (CCA) to capture the temporal evolution of clusters. Based on this extended canonical correlation framework, we define the spatio-temporal graph Laplacian and investigate its spectral properties. We connect these concepts to dynamical systems theory via transfer operators, and illustrate the advantages of our method on benchmark graphs by comparison with existing methods. We show that the spatio-temporal graph Laplacian allows for a clear interpretation of cluster structure evolution over time for directed and undirected graphs
An Application of Modified S-CLSVOF Method to Kelvin-Helmholtz Instability and Comparison with Theoretical Result
No full textThis study focuses on validating a two-phase flow solver based on the modified Simple Coupled Level Set and Volume of Fluid method (Uchihashi et al. (2023)) through viscous Kelvin-Helmholtz instability simulations. Our numerical simulation results are compared with the ones given by Funada and Joseph (2001) to provide reliable predictions of interface behavior under the influence of viscosity. The primary goal is to accurately assess the solver's ability to replicate theoretical analysis of interface behaviors under various conditions. First, the wave between two fluids of identical density is calculated. In addition, the effect of surface tension is investigated. By comparing growth rates, numerical simulations obtain well-agreements with the analytical results on the effect of the fluid viscosity, the wave number, and the surface tension. Finally, fluid density is changed to an air-water system. When relative velocity U is smaller than the criteria of relative velocity U_c given by analytical solutions, the wave is not broken. However, waves are splashed into droplets in the condition of U>U_c. This result agrees with the analysis by Funada and Joseph (2001). These findings provide a robust framework for applying the solver to more complex two-phase flow problems, supporting advancements in numerical simulations of fluid interfaces
Risk aversion can promote cooperation
No full textCooperative dynamics are central to our understanding of many phenomena in living and complex systems. However, we lack a universal mechanism to explain the emergence of cooperation. We present a novel framework for modelling social dilemma games with an arbitrary number of players by combining reaction networks, methods from quantum mechanics applied to stochastic complex systems, game theory and stochastic simulations of molecular reactions. Using this framework, we propose a novel and robust mechanism for cooperation based on risk aversion that leads to cooperative behaviour in population games. Rather than individuals seeking to maximise payouts in the long run, individuals seek to obtain a minimum set of resources with a given level of confidence and in a limited time span. We show that this mechanism can lead to the emergence of new equilibria in a range of social dilemma games
Solving the n-Queens Problem in Higher Dimensions
No full textHow many mutually non-attacking queens can be placed on a d-dimensional chessboard of size n? The n-queens problem in higher dimensions is a generalization of the well-known n-queens problem. We present an integer programming formulation of the n-queens problem in higher dimensions and several strengthenings through additional valid inequalities. Compared to recent benchmarks, we achieve a speedup in computational time between 15–70x over all instances of the integer programs. Our computational results prove optimality of certificates for several large instances. Breaking additional, previously unsolved instances with the proposed methods is likely possible. On the primal side, we further discuss heuristic approaches to constructing solutions that turn out to be optimal when compared to the IP
An accurate mean-field equation for voter model dynamics on scale-free networks
No full textUnderstanding the emergent macroscopic behavior of dynamical systems on networks is a crucial but challenging task. One of the simplest and most effective methods to construct a reduced macroscopic model is given by mean-field theory. The resulting approximations perform well on dense and homogeneous networks but poorly on scale-free networks, which, however, are more realistic in many applications. In this paper, we introduce a modified version of the mean-field approximation for voter model dynamics on scale-free networks. The two main deviations from classical theory are that we use degree-weighted shares as coarse variables and that we introduce a correlation factor that can be interpreted as slowing down dynamics induced by interactions. We observe that the correlation factor is only a property of the network and not of the state or of parameters of the process. This approach achieves a significantly smaller approximation error than standard methods without increasing dimensionality
