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The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
We describe a parallel solver for the discretized weakly singular space-time boundary integral equation of the spatially two-dimensional heat equation. The global space-time nature of the system matrices leads to improved parallel…
Linear programming is used as a standard tool for optimising unit commitment or power flows in energy supply systems. For heat supply systems, however, it faces a relevant limitation: For them, energy yield depends on the output…
We discuss the application of techniques of quantum estimation theory and quantum metrology to thermometry. The ultimate limit to the precision at which the temperature of a system at thermal equilibrium can be determined is related to the…
The equations of the temperature-accelerated molecular dynamics (TAMD) method for the calculations of free energies and partition functions are analyzed. Specifically, the exponential convergence of the law of these stochastic processes is…
We present an adaptive multi-GPU Exchange Monte Carlo method designed for the simulation of the 3D Random Field Model. The algorithm design is based on a two-level parallelization scheme that allows the method to scale its performance in…
The maximum entropy method is shown to be a special limit of the stochastic analytic continuation method introduced by Sandvik [Phys. Rev. B 57, 10287 (1998)]. We employ a mapping between the analytic continuation problem and a system of…
We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large…
OpenMP parallelization of multiple precision Taylor series method is proposed. A very good parallel performance scalability and parallel efficiency inside one computation node of a CPU-cluster is observed. We explain the details of the…
Decoupling approach presents a novel solution/alternative to the highly time-consuming fluid-thermal-structural simulation procedures when thermal effects and resultant displacements on machine tools are analyzed. Using high dimensional…
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we…
We propose a new global optimization method ({\em Simulated Tempering}) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated…
Integer Linear Programming (ILP) serves as a versatile framework for modeling a wide range of combinatorial optimization problems, typically addressed by sophisticated exact solvers or heuristics. While learning-based approaches have…
Temperature of a finite-sized system fluctuates due to the thermal fluctuations. However, a systematic mathematical framework for measuring or estimating the temperature is still underdeveloped. Here, we incorporate the estimation theory in…
Diversity is an essential metric for evaluating the creativity of outputs generated by language models. Temperature-based sampling is a common strategy to increase diversity. However, for tasks that require high precision, e.g.,…
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…
We present a novel class of methods to compute functions of matrices or their action on vectors that are suitable for parallel programming. Solving appropriate simple linear systems of equations in parallel (or computing the inverse of…
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…
The concepts of weighted reciprocal of temperature and weighted thermal flux are proposed for a heat engine operating between two heat baths and outputting mechanical work. With the aid of these two concepts, the generalized thermodynamic…
We study full counting statistics for transferred heat and entropy production between multi-terminal systems in absence of a finite junction. The systems are modelled as collections of coupled harmonic oscillators which are kept at…