Engineering topics

Hummer, Gerhard

Publications and source records attributed to Hummer, Gerhard.

3 records

DOE OSTI2023

Martini 3 Coarse-Grained Force Field for Cholesterol

Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. In conclusion, the proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Membrane fusion and drug delivery with carbon nanotube porins

Significance The plasma membrane protects cell content from the outer environment. Overcoming this obstacle and delivering drugs efficiently into cells still remain a major hurdle for modern pharmacology and medicine. We developed and demonstrated a simple nanomaterial platform—a dimer of small-diameter carbon nanotube porins (CNTPs)—which functions as a potent membrane fusogen. Molecular simulations revealed a distinct fusion mechanism. CNTP-studded vesicles loaded with a chemotherapeutic agent, doxorubicin, delivered the drug to cancer cells, killing a majority of them. Our work provides new opportunities for understanding membrane fusion mechanisms, designing synthetic fusogens, and developing simple and efficient drug carriers for delivery of therapeutics and vaccines.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems

During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. In this work, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗