A5004559776- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Protein purification and stability
- RNA and protein synthesis mechanisms
- Monoclonal and Polyclonal Antibodies Research
- Pickering emulsions and particle stabilization
- Cell Image Analysis Techniques
- Protein Structure and Dynamics
- Microfluidic and Bio-sensing Technologies
- Escherichia coli research studies
- Blood properties and coagulation
- Diffusion and Search Dynamics
- Material Science and Thermodynamics
- Mathematical Dynamics and Fractals
- RNA modifications and cancer
- Advanced Mathematical Theories and Applications
- Material Dynamics and Properties
- Viral Infectious Diseases and Gene Expression in Insects
- Gene Regulatory Network Analysis
- Surfactants and Colloidal Systems
- Rheology and Fluid Dynamics Studies
Stanford University
2022-2025
Massachusetts Institute of Technology
2018
The crowded bacterial cytoplasm is composed of biomolecules that span several orders magnitude in size and electrical charge. This complexity has been proposed as the source rich spatial organization apparent anomalous diffusion intracellular components, although this not tested directly. Here, we use biplane microscopy to track 3D motion self-assembled genetically encoded multimeric nanoparticles (bGEMs) with tunable (20 50 nm) charge (−3,240 +2,700 e) live Escherichia coli cells. To probe...
Therapeutic antibody design is a complex multi-property optimization problem that traditionally relies on expensive search through sequence space. Here, we introduce "Lab-in-the-loop," paradigm shift for orchestrates generative machine learning models, multi-task property predictors, active ranking and selection, in vitro experimentation semi-autonomous, iterative loop. By automating the of variants, prediction, selection designs to assay lab, ingestion data, enable holistic, end-to-end...
Reversible self-association of therapeutic antibodies is a key factor in high protein solution viscosities. In the present work, coarse-grained computational model accounting for electrostatic, dispersion, and long-ranged hydrodynamic interactions two monoclonal applied to understand nature self-association, predicting microstructure resulting transport properties solution. For proteins investigated, structure across range conditions shows quantitative agreement with neutron-scattering...
ABSTRACT Protein therapeutic design and property prediction are frequently hampered by data scarcity. Here we propose a new model, DyAb, that addresses these issues leveraging pair-wise representation to predict differences in protein properties, rather than absolute values. DyAb is built on top of pre-trained language model achieves Spearman rank correlation up 0.85 binding affinity across molecules targeting three different antigens (EGFR, IL-6, an internal target), given as few 100...
ABSTRACT The crowded bacterial cytoplasm is comprised of biomolecules that span several orders magnitude in size and electrical charge. This complexity has been proposed as the source rich spatial organization apparent anomalous diffusion intracellular components, although this not tested directly. Here, we use biplane microscopy to track 3D motion self-assembled Genetically Encoded Multimeric nanoparticles (bGEMs) with tunable (20 50 nm) charge (−2160 +1800 e) live Escherichia coli cells....
Abstract Research on protein-protein interaction (PPIs) tends to focus high affinity interactions. Weaker interactions ( K d >1 μM ) recently understood as contributing intracellular phase separation suggest that even-weaker PPIs might also matter in as-yet unknown ways. However, ultra-weak mM are not readily accessible by vivo techniques. Here we use protein electrostatics estimate PPI strengths and spatially-resolved dynamic simulations investigate the potential impacts of within dense...
ABSTRACT Actively translating ribosomes must wait after each elongation step for a new ternary complex (EF-Tu·aa-tRNA·GTP) to be delivered, facilitating rapid codon recognition testing and continued elongation. We recently showed that this time rate-limits in Escherichia coli due competitive combinatoric search through crowded cytoplasm by thousands of E. ’s 42 unique complexes. Here, we investigate whether L12 subunits on ribosomes’ surfaces pool translation molecules reduce time. To do so,...
Attractive colloidal dispersions, suspensions of fine particles which aggregate and frequently form a space spanning elastic gel are ubiquitous materials in society with wide range applications. The networks these can exist mode free settling when the network weight exceeds its compressive yield stress. An equivalent state occurs is held fixed place used as filter through suspending fluid pumped. In either scenario, hydrodynamic instabilities leading to loss integrity occur. Experimental...