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Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
While large language models (LLMs) have demonstrated remarkable performance across diverse tasks, they fundamentally lack self-awareness and frequently exhibit overconfidence, assigning high confidence scores to incorrect predictions.…
We present in this paper a new approach for polyphonic music transcription using evolution strategies (ES). Automatic music transcription is a complex process that still remains an open challenge. Using an audio signal to be transcribed as…
Controlling complex networks is of paramount importance in science and engineering. Despite recent efforts to improve controllability and synchronous strength, little attention has been paid to the speed of pinning synchronizability (rate…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…
Parameterless stopping criteria for recursive polynomial expansions to construct the density matrix in electronic structure calculations are proposed. Based on convergence order estimation the new stopping criteria automatically and…
Behavioral patterns captured in embeddings learned from interaction data are pivotal across various stages of production recommender systems. However, in the initial retrieval stage, practitioners face an inherent tradeoff between embedding…
Deep learning models have been proposed for automatic polyp detection and precise segmentation of polyps during colonoscopy procedures. Although these state-of-the-art models achieve high performance, they often require a large number of…
We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…
The performance of convolutional neural networks (CNN) depends heavily on their architectures. Transfer learning performance of a CNN relies quite strongly on selection of its trainable layers. Selecting the most effective update layers for…
Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise…
Achieving practical quantum advantage requires a classical decoding algorithm to identify and correct faults during computation. This classical decoding algorithm must deliver both accuracy and speed, but in what combination? When is a…
Fitting models to data is an important part of the practice of science. Advances in machine learning have made it possible to fit more -- and more complex -- models, but have also exacerbated a problem: when multiple models fit the data…
We consider a multiple hypothesis testing setting where the hypotheses are ordered and one is only permitted to reject an initial contiguous block, H_1,\dots,H_k, of hypotheses. A rejection rule in this setting amounts to a procedure for…
The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the…
Eukaryotic cells perform chemotaxis by determining the direction of chemical gradients based on stochastic sensing of concentrations at the cell surface. To examine the efficiency of this process, previous studies have investigated the…
A class of two-bit bit flipping algorithms for decoding low-density parity-check codes over the binary symmetric channel was proposed in [1]. Initial results showed that decoders which employ a group of these algorithms operating in…