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In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…

Machine Learning · Computer Science 2026-04-16 Peter Zhiping Zhang , Jeffrey D. Varner

We present a novel framework for chemical learning based on Competitive Dimerization Networks (CDNs) - systems in which multiple molecular species, e.g. proteins or DNA/RNA oligomers, reversibly bind to form dimers. We show that these…

Statistical Mechanics · Physics 2025-06-18 Alexei V. Tkachenko , Bortolo Matteo Mognetti , Sergei Maslov

Silica is an abundant component of the Earth whose crystalline polymorphs play key roles in its structure and dynamics. As the simplest silicates, understanding pure silica is a prerequisite to understanding the rocky part of the Earth, its…

Recently developed single-phase concentrated solid-solution alloys (CSAs) contain multiple elemental species in high concentrations with different elements randomly arranged on a crystalline lattice. These chemically disordered materials…

Computational Physics · Physics 2025-02-19 K. Frydrych , F. J. Dominguez-Gutierrez , M. J. Alava , S. Papanikolaou

The deliberate control over the spatial arrangement of nanostructures is the desired goal for many applications as e.g. in data storage, plasmonics or sensor arrays. Here we present a novel method to assist the self-assembly process of…

Reinforcement of elastomers by colloidal nanoparticles is an important application where microstructure needs to be understood - and if possible controlled - if one wishes to tune macroscopic mechanical properties. Here the…

Soft Condensed Matter · Physics 2007-05-23 Julian Oberdisse , Peter Hine , Wim Pyckhout-Hintzen

The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…

Layers obtained by drying a colloidal dispersion of silica spheres are found to be a good benchmark to test the elastic behaviour of porous media, in the challenging case of high porosities and nano-sized microstructures. Classically used…

Soft Condensed Matter · Physics 2018-06-24 Arnaud Lesaine , Daniel Bonamy , Georges Gauthier , Cindy Rountree , Véronique Lazarus

Conventionally, high-throughput computational materials searches start from an input set of bulk compounds extracted from material databases, and this set is screened for candidate materials for specific applications. In contrast, many…

Materials Science · Physics 2023-04-11 Rachel Woods-Robinson , Matthew K. Horton , Kristin A. Persson

Discotic ionic liquid crystals (DILCs) consist of self-assembled superdiscs of cations and anions that spontaneously stack in linear columns with high one-dimensional ionic and electronic charge mobility, making them prominent model systems…

Imaging individual conformational instances of generic, inhomogeneous, transient or intrinsically disordered protein systems at the single molecule level in situ is one of the notable challenges in structural biology. Present techniques…

Quantum Physics · Physics 2021-12-08 Viktor S. Perunicic , Muhammad Usman , Charles D. Hill , Lloyd C. L. Hollenberg

Self-supervised learning (SSL) has emerged as an effective paradigm for deriving general representations from vast amounts of unlabeled data. However, as real-world applications continually integrate new content, the high computational and…

Machine Learning · Computer Science 2024-03-28 Wenzhuo Liu , Fei Zhu , Cheng-Lin Liu

Porous magnetic silica beads are promising materials for biological and environmental applications due to their enhanced adsorption and ease of recovery. This work aims to develop a new, inexpensive and environmentally friendly approach…

Applied Physics · Physics 2020-05-21 David Franck Frederic Brossault , Alexander F. Routh

The directed self-assembly of colloidal nanoparticles (NPs) using external fields guides the formation of sophisticated hierarchical materials but becomes less effective with decreasing particle size. As an alternative, electron-beam-driven…

Soft Condensed Matter · Physics 2024-09-13 Jonathan G. Raybin , Ethan J. Dunsworth , Veronica Guo , Naomi S. Ginsberg

Bottom-up assembly of nanocrystals (NCs) into ordered arrays, or superlattices (SLs), is a promising route to design materials with new functionalities, but the degree of control over assembly into functional structures remains challenging.…

Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…

We present a selection of x-ray and neutron diffraction patterns of spherical (He, Ar), dumbbell- (N2, CO), and chain-like molecules (n-C9H20, n-C19H40) solidified in nanopores of silica glass (mean pore diameter 7nm). These patterns allow…

Mesoscale and Nanoscale Physics · Physics 2007-05-23 Patrick Huber , Klaus Knorr

The process of self-assembly is guided by the minimization of free energy, which limits the symmetries available for assembly and ultimately the usefulness of devices fabricated in this fashion. Here, we demonstrate experimentally for the…

While clustering is ubiquitously used across science and industry, uncertainty in cluster assignments is rarely quantified with rigorous guarantees. We propose a novel conformal inference framework for clustering that returns confidence…

Methodology · Statistics 2026-04-13 YoonHaeng Hur , Anirban Nath , Genevera Allen

High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…

Biological Physics · Physics 2009-10-31 G. Getz , E. Levine , E. Domany , M. Q. Zhang
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