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Parametrized 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 stymied by the presence of local minima in the parameter landscape. One approach to mitigate this issue is to use parallel tempering methods, and in this work, we focus on the role played by the temperature distribution of the parallel tempering replicas. Using an adaptive method that adjusts the temperatures in order to equate the exchange probability between neighboring replicas, we show that this temperature optimization can significantly increase the success rate of the variational algorithm with negligible computational cost by eliminating bottlenecks in the replicas' random walk. We demonstrate this using two different neural networks, a restricted Boltzmann machine and a feedforward network, which we use to study a toy problem based on a permutation invariant Hamiltonian with a pernicious local minimum and the J_{1}-J_{2} model on a rectangular lattice.
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http://dx.doi.org/10.1103/PhysRevE.111.055306 | DOI Listing |
Nucleic Acids Res
September 2025
Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic.
RNA G-quadruplexes (rG4s) are emerging as vital structural elements involved in processes like gene regulation, translation, and genome stability. Found in untranslated regions of messenger RNAs (mRNAs), they influence translation efficiency and mRNA localization. Additionally, rG4s of long noncoding RNAs and telomeric RNA play roles in RNA processing and cellular aging.
View Article and Find Full Text PDFQuantum Mach Intell
September 2025
USRA Research Institute for Advanced Computer Science (RIACS), Moffett Field, CA USA.
We discuss guidelines for evaluating the performance of parameterized stochastic solvers for optimization problems, with particular attention to systems that employ novel hardware, such as digital quantum processors running variational algorithms, analog processors performing quantum annealing, or coherent Ising machines. We illustrate through an example a benchmarking procedure grounded in the statistical analysis of the expectation of a given performance metric measured in a test environment. In particular, we discuss the necessity and cost of setting parameters that affect the algorithm's performance.
View Article and Find Full Text PDFJ Chem Phys
September 2025
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Gold nanocrystals have been widely used in sensing and medicine, where nanocrystal shape can profoundly influence properties. To describe and predict the structure and properties of Au nanomaterials, first-principles studies are the most accurate. Force fields can provide effective surrogates for first-principles calculations, and in the case of Au, many such force fields exist.
View Article and Find Full Text PDFAnn Appl Stat
September 2025
Department of Statistics and Data Sciences, The University of Texas at Austin.
Observational zero-inflated count data arise in a wide range of areas such as genomics. One of the common research questions is to identify causal relationships by learning the structure of a sparse directed acyclic graph (DAG). While structure learning of DAGs has been an active research area, existing methods do not adequately account for excessive zeros and therefore are not suitable for modeling zero-inflated count data.
View Article and Find Full Text PDFbioRxiv
July 2025
Department of Chemical and Biomedical Engineering, University of Wyoming, Laramie, WY 82071, United States.
The dynamic coupling between chromatin organization and biomolecular condensates is governed by chromatin-binding proteins, yet the structural mechanisms by which these proteins modulate nucleosome interactions across spatial and organizational scales remain poorly understood. In this work, using high-resolution sequence-specific coarse-grained models combined with well-tempered metadynamics and parallel tempering, we investigate how heterochromatin protein 1α (HP1α) and a truncated construct of Polyhomeotic-like protein (tPHC3) influence the stability and folding pathways of tetra-nucleosomes, a minimal yet functionally informative chromatin model, under dilute and dense-phase conditions. While these proteins are known to drive distinct nuclear condensates their differential impact on chromatin topology and folding dynamics remains unclear.
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