The synthesis of complex materials through the self-assembly of particles at the nanoscale provides opportunities for the realization of novel material properties. However, the inverse design process to create experimentally feasible interparticle interaction strategies is uniquely challenging. Standard methods for the optimization of isotropic pair potentials tend toward overfitting, resulting in solutions with too many features and length scales that are challenging to map to mechanistic models. Here we introduce a method for the optimization of simple pair potentials that minimizes the relative entropy of the complex target structure while directly considering only those length scales most relevant for self-assembly. Our approach maximizes the relative information of a target pair distribution function with respect to an ansatz distribution function via an iterative update process. During this process, we filter high frequencies from the Fourier spectrum of the pair potential, resulting in interaction potentials that are smoother and simpler in real space and therefore likely easier to make. We show that pair potentials obtained by this method assemble their target structure more robustly with respect to optimization method parameters than potentials optimized without filtering.
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http://dx.doi.org/10.1063/1.5063802 | DOI Listing |
Biotechniques
December 2024
Laboratorio de Parasitología Molecular, Vicerrectoría de Investigaciones, Universidad El Bosque, Bogotá, Colombia.
In 2006, a PCR method was introduced to subtype by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non- sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from cultures, limiting its sensitivity when used directly with stool samples.
View Article and Find Full Text PDFRedox Biol
December 2024
Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.
The increase in early-stage cancers, particularly gastrointestinal, breast and kidney cancers, has been linked to lifestyle changes such as consumption of processed foods and physical inactivity, which contribute to obesity and diabetes - major cancer risk factors. Conventional treatments such as chemotherapy and radiation often lead to severe long-term side effects, including secondary cancers and tissue damage, highlighting the need for new, safer and more effective therapies, especially for young patients. Weak electromagnetic fields (WEMF) offer a promising non-invasive approach to cancer treatment.
View Article and Find Full Text PDFRedox Biol
December 2024
Graduate Program in Toxicology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. Electronic address:
Alcohol consumption induces hepatocyte damage through complex processes involving oxidative stress and disrupted metabolism. These factors alter proteomic and epigenetic marks, including alcohol-induced protein acetylation, which is a key post-translational modification (PTM) that regulates hepatic metabolism and is associated with the pathogenesis of alcohol-associated liver disease (ALD). Recent evidence suggests lysine acetylation occurs when a proximal cysteine residue is within ∼15 Å of a lysine residue, referred to as a cysteine-lysine (Cys-Lys) pair.
View Article and Find Full Text PDFBiochem Biophys Res Commun
December 2024
Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA. Electronic address:
Hemoglobin and myoglobin are known to undergo autoxidation, in which the oxyferrous form of the heme is oxidized to the ferric state by O. Dehaloperoxidase-A (DHP-A), a multifunctional catalytic hemoglobin from Amphitrite ornata is an exception and is observed to undergo the reverse process, during which the ferric heme is spontaneously reduced to the oxyferrous form under aerobic conditions. The high reduction potential of DHP (+202 mV at pH 7.
View Article and Find Full Text PDFJ Am Chem Soc
December 2024
Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States.
Designing catalysts with well-defined active sites with chemical functionality responsive to visible light has significant potential for overcoming scaling relations limiting chemical reactions over heterogeneous catalyst surfaces. Visible light can be leveraged to facilitate the removal of strongly bound species from well-defined single cationic sites (Rh) under mild conditions (323 K) when they are incorporated within a photoactive perovskite oxide (Rh-doped SrTiO). CO, a key intermediate in many chemistries, forms stable geminal dicarbonyl Rh complexes (Rh(CO)), that could act as site blockers or poisons during a catalytic cycle.
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