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Lipid Bilayers

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A machine learning approach to estimation of phase diagrams for three-component lipid mixtures.

Biochimica et biophysica acta. Biomembranes
The plasma membrane of eukaryotic cells is commonly believed to contain ordered lipid domains. The interest in understanding the origin of such domains has led to extensive studies on the phase behavior of mixed lipid systems. Three-component phase d...

Artificial neural networks for the inverse design of nanoparticles with preferential nano-bio behaviors.

The Journal of chemical physics
Safe and efficient use of ultrasmall nanoparticles (NPs) in biomedicine requires numerous independent conditions to be met, including colloidal stability, selectivity for proteins and membranes, binding specificity, and low affinity for plasma protei...

Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables.

The Journal of chemical physics
Understanding the permeation of biomolecules through cellular membranes is critical for many biotechnological applications, including targeted drug delivery, pathogen detection, and the development of new antibiotics. To this end, computer simulation...

Parallel transmission in a synthetic nerve.

Nature chemistry
Bioelectronic devices that are tetherless and soft are promising developments in medicine, robotics and chemical computing. Here, we describe bioinspired synthetic neurons, composed entirely of soft, flexible biomaterials, capable of rapid electroche...

Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach.

Biophysical journal
Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a li...

Application of Generative Artificial Intelligence in Predicting Membrane Partitioning of Drugs: Combining Denoising Diffusion Probabilistic Models and MD Simulations Reduces the Computational Cost to One-Third.

Journal of chemical theory and computation
The optimal interaction of drugs with plasma membranes and membranes of subcellular organelles is a prerequisite for desirable pharmacology. Importantly, for drugs targeting the transmembrane lipid-facing sites of integral membrane proteins, the rela...

Topological Learning Approach to Characterizing Biological Membranes.

Journal of chemical information and modeling
Biological membranes play key roles in cellular compartmentalization, structure, and its signaling pathways. At varying temperatures, individual membrane lipids sample from different configurations, a process that frequently leads to higher-order pha...

An active machine learning discovery platform for membrane-disrupting and pore-forming peptides.

Physical chemistry chemical physics : PCCP
Membrane-disrupting and pore-forming peptides (PFPs) play a substantial role in bionanotechnology and can determine the life and death of cells. The control of chemical and ion transport through cell membranes is essential to maintaining concentratio...

Investigating the Bromoform Membrane Interactions Using Atomistic Simulations and Machine Learning: Implications for Climate Change Mitigation.

The journal of physical chemistry. B
Methane emissions from livestock contribute to global warming. Seaweeds used as food additive offer a promising emission mitigation strategy because seaweeds are enriched in bromoform─a methanogenesis inhibitor. Therefore, understanding bromoform sto...

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence.

The Journal of chemical physics
Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the bio...