Search · four archives
Search · four archives
11 papers · ranked by Valyu relevance
Martin Schlather
Since the calculation of a genomic relationship matrix needs a large number of arithmetic operations, fast implementations are of interest. Our fastest algorithm is more accurate and 25× faster than a AVX double precision floating-point implementation.
Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai
The analysis of secondary structures is essential to understanding the function of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distribution of secondary structures. Existing methods, however, are not applicable to long RNAs owing to their high computational complexity.…
Koichi Miyamoto, Naoki Yamamoto, Yasubumi Sakakibara
We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The…
David Brust, Johannes J. Brust
Grouping samples with low prevalence of positives into pools and testing these pools can achieve considerable savings in testing resources compared with individual testing in the context of COVID-19. We review published pooling matrices, which encode the assignment of samples into pools and describe decoding…
Authors not listed
We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We…
Zhihao Lan, WanZhen Liang
The variational quantum eigensolver (VQE) algorithm can simulate the chemical systems such as molecules in the noisy intermediate-scale quantum devices and shows promising applications in quantum chemistry simulations. The accuracy and computational cost of the VQE simulations are determined by the underlying Ansätze.…
Eric Hermes, Khachik Sargsyan, Habib Najm, Judit Zádor
We present a new algorithm for the optimization of molecular structures to saddle points on the potential energy surface using a redundant internal coordinate system. This algorithm automates the procedure of defining the internal coordinate system, including the handling of linear bending angles, e.g. through the…
Alexandre Zénon, Samuel Salvaggio, Michael Andres
The assumption that the brain relies on Bayesian inference has been successful in accounting for many behavioural and neurophysiological observations, but to date, dependence on such mechanism has not been assessed in the context of arithmetic. Bayesian inference implies the representation of uncertainty and reliance…
MARCO TODISCO
Determining the distribution of multiple chemical species at equilibrium for a given system is a common problem that must be routinely addressed by scholars. While simple systems consisting of a few species and reactions can be solved manually, most of these problems require the definition and solution of higher-order…
Pavel Pokhilko, Evgeny Epifanovsky, Anna I. Krylov
Using single precision floating point representation reduces the size of data and computation time by a factor of two relative to double precision conventionally used in electronic structure programs. For large-scale calculations, such as those encountered in many-body theories, reduced memory footprint alleviates…
Authors not listed
The SCF part of the HF-SCF method is responsible for finding the ground state as the global minimum of the one-determinant approximation of the electronic energy, which is a 4th order multivariable polynomial of the LCAO coefficients and Lagrange multipliers. In this work we replace this SCF part with algebraic…