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Thermodynamics and Modeling of Collective Effects in the Organic Ligand Shell of Colloidal Quantum Dots.
Acc Chem Res
January 2025
Department of Chemistry , University of California, Berkeley, California 94720, United States.
ConspectusColloidal nanocrystals are an interesting platform for studying the surface chemistry of materials due to their high surface area/volume ratios, which results in a large fraction of surface atoms. As synthesized, the surfaces of many colloidal nanocrystals are capped by organic ligands that help control their size and shape. While these organic ligands are necessary in synthesis, it is often desirable to replace them with other molecules to enhance their properties or to integrate them into devices.
View Article and Find Full Text PDFFriction in soft biological systems and surface self-organization: the role of viscoelasticity.
Biophys Rev
December 2024
Department of Physics, Lancaster University, Lancaster, LA1 4YB UK.
Friction is a critical factor in the proper functioning of human organs as well as in the potential development of disease. It is also important for the design of diagnostic and interventional medical devices. Nanoscale surface roughness, viscoelastic or plastic deformations, wear, and lubrication all influence the functions of individual cells.
View Article and Find Full Text PDFMoonlighting antibiotics: the extra job of modulating biofilm formation.
Trends Microbiol
January 2025
Laboratorio de Estructura y Fisiología de Biofilms Microbianos, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000) Rosario, Argentina. Electronic address:
The widespread use of antibiotics to treat bacterial infections has led to the common perception that their only function is to inhibit growth or kill bacteria. However, it has become clear that when antibiotics reach susceptible bacteria at non-lethal concentrations, they perform additional functions that significantly impact bacterial physiology, shaping both individual and collective behaviors. A key bacterial behavior influenced by sub-lethal antibiotic doses is biofilm formation, a multicellular, surface-associated mode of growth.
View Article and Find Full Text PDFProtein Target Search Diffusion-association/dissociation Free Energy Landscape around DNA Binding Site with Flanking Sequences.
Biophys J
January 2025
Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, USA. Electronic address:
In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements.
View Article and Find Full Text PDFEnhanced sampling of robust molecular datasets with uncertainty-based collective variables.
J Chem Phys
January 2025
Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Generating a dataset that is representative of the accessible configuration space of a molecular system is crucial for the robustness of machine-learned interatomic potentials. However, the complexity of molecular systems, characterized by intricate potential energy surfaces, with numerous local minima and energy barriers, presents a significant challenge. Traditional methods of data generation, such as random sampling or exhaustive exploration, are either intractable or may not capture rare, but highly informative configurations.
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