A5087654509- Cellular Mechanics and Interactions
- Protein Structure and Dynamics
- Force Microscopy Techniques and Applications
- Machine Learning in Materials Science
- Cardiomyopathy and Myosin Studies
- Material Dynamics and Properties
- Spectroscopy and Quantum Chemical Studies
- Enzyme Structure and Function
- Microtubule and mitosis dynamics
- Polymer Surface Interaction Studies
- Micro and Nano Robotics
- Advanced Fluorescence Microscopy Techniques
- RNA Research and Splicing
- Pickering emulsions and particle stabilization
- Theoretical and Computational Physics
- Genetics, Bioinformatics, and Biomedical Research
- Mass Spectrometry Techniques and Applications
- Adhesion, Friction, and Surface Interactions
- Advanced Thermodynamics and Statistical Mechanics
- Mechanical and Optical Resonators
- Advanced Chemical Physics Studies
- RNA and protein synthesis mechanisms
- Molecular Junctions and Nanostructures
- Lipid Membrane Structure and Behavior
- Biomedical Text Mining and Ontologies
New York University
2018-2025
Simons Foundation
2022-2023
University of Chicago
2008-2020
Chicago Institute for Psychoanalysis
2015-2020
Courant Institute of Mathematical Sciences
2020
Alexandria University
2019
University of Illinois Chicago
2018
Columbia University
2012-2014
School of the Art Institute of Chicago
2008-2010
In this work, we investigate the question: do code-generating large language models know chemistry? Our results indicate, mostly yes.
In computational physics, chemistry, and biology, the implementation of new techniques in shared open-source software lowers barriers to entry promotes rapid scientific progress. However, effectively training users presents several challenges. Common methods like direct knowledge transfer in-person workshops are limited reach comprehensiveness. Furthermore, while COVID-19 pandemic highlighted benefits online training, traditional tutorials can quickly become outdated may not cover all...
It has been demonstrated recently that supercooled liquids sharing simple structural features (e.g. pair distribution functions) may exhibit strikingly distinct dynamical behavior. Here we show a more subtle feature correlates with relaxation times in three simulated systems have nearly identical radial functions but starkly different In particular, for the first time determine thermodynamic ``point-to-set'' length scale several canonical model and demonstrate quantitative connection between...
The fission yeast actin cytoskeleton is an ideal, simplified system to investigate fundamental mechanisms behind cellular self-organization. By focusing on the stabilizing protein tropomyosin Cdc8, bundling fimbrin Fim1, and severing coffin Adf1, we examined how their pairwise collective interactions with filaments regulate activity segregation functionally diverse F-actin networks. Utilizing multi-color TIRF microscopy of in vitro reconstituted networks, observed characterized two distinct...
Significance Actin filament nucleation by Arp2/3 complex must be triggered activators like WASP family proteins. Understanding how proteins activate has been a major challenge due to lack of high-resolution structures the in an activated state. We determined (∼3.9 Å) structure WASP-activated at branch junction and used biochemical, cell biological, molecular dynamic simulations understand mechanism WASP-mediated activation. This work shows detail contacts between fully complex, nucleated...
We investigate the connection between local structure and dynamical heterogeneity in supercooled liquids. Through study of four different models, we show that correlation a particle's mobility degree order nearby regions is highly system dependent. Our results suggest dynamics weak or absent systems conform well to mean-field picture glassy strong those deviate from this paradigm. Finally, role order-agnostic point-to-set correlations reveal they provide similar information content measures,...
Cytokinesis physically separates dividing cells by forming a contractile actomyosin ring. The fission yeast ring has been proposed to assemble Search-Capture-Pull-Release from cytokinesis precursor nodes that include the molecular motor type-II myosin Myo2 and actin assembly factor formin Cdc12. By successfully reconstituting Search-Capture-Pull in vitro, we discovered Cdc12 is mechanosensor, whereby pulling on formin-bound filaments inhibits Cdc12-mediated assembly. We mapped...
Determining the optimal number and identity of structural clusters from an ensemble molecular configurations continues to be a challenge. Recent clustering methods have focused on use internal coordinates due innate rotational translational invariance these features. The vast possible necessitates feature space supervision step make tractable but yields protocol that can system type-specific. Particle positions offer appealing alternative suffer lack invariance, as well perceived...
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces good reaction coordinate between those states. Atomic coordinates macromolecule are direct representation macromolecular configuration, and yet, they not used enhanced sampling studies due lack rotational translational invariance. We resolve issue using the technique our prior whereby molecular configuration is considered member an equivalence...
The actomyosin contractile ring is a network of cross-linked actin filaments that facilitates cytokinesis in dividing cells. Contractile formation has been well characterized Schizosaccharomyces pombe, which the cross-linking protein α-actinin SpAin1 bundles filament network. However, specific biochemical properties and whether they are tailored for not known. Therefore we purified quantified its ability to dynamically bind bundle vitro using combination bulk sedimentation assays direct...
We study the relaxation dynamics of a binary Lennard-Jones liquid in presence an amorphous wall generated from equilibrium particle configurations. In qualitative agreement with results presented Nature Phys. {\bf 8}, 164 (2012) for harmonic spheres, we find that our mixture shows saturation dynamical length scale close to mode-coupling temperature $T_c$. Furthermore show that, due broken symmetry imposed by wall, signatures additional change become apparent at well above provide evidence...
Abstract The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown crosslinking α-actinin fascin segregate distinct domains in single bundles with molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, giant unilamellar vesicles (GUVs), we show physical confinement cause these to form much more complex structures, including rings asters at GUV...
Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding are free to diffuse and rearrange on surface, giving rise spontaneous control over number droplet-droplet bonds, i.e., valence, as function concentration binders. This type valence has been realized experimentally by tuning interaction strength between DNA-coated emulsion droplets. Optimizing two yields droplet polymer chains, termed 'colloidomers', which have...
Our ability to efficiently sample conformational transitions between two known states of a biomolecule using collective variable (CV) based sampling depends strongly on the choice CV. We previously reported data-driven approach clustering biomolecular configurations with probabilistic model termed ShapeGMM. ShapeGMM is Gaussian Mixture Model in cartesian coordinates, means and covariances each cluster representing harmonic approximation ensemble around metastable state. subsequently showed...
Many biological processes, including cell division, growth, and motility, rely on rapid remodeling of the actin cytoskeleton filament severing by regulatory protein cofilin. Phosphorylation vertebrate cofilin at Ser-3 regulates both binding severing. Substitution serine with aspartate position 3 (S3D) is widely used to mimic phosphorylation in cells vitro. The S3D substitution weakens filaments, it presumed that subsequent reduction occupancy inhibits severing, but this hypothesis has...