A5022576195- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- DNA and Nucleic Acid Chemistry
- Block Copolymer Self-Assembly
- Advanced Polymer Synthesis and Characterization
- Theoretical and Computational Physics
- Bacteriophages and microbial interactions
- RNA Research and Splicing
- Material Dynamics and Properties
- Polymer crystallization and properties
- Machine Learning in Materials Science
- Nanopore and Nanochannel Transport Studies
- Protein Structure and Dynamics
- Rheology and Fluid Dynamics Studies
- Polymer Surface Interaction Studies
- Advanced biosensing and bioanalysis techniques
- Advanced Materials and Mechanics
- Gold and Silver Nanoparticles Synthesis and Applications
- Diatoms and Algae Research
- Chromosomal and Genetic Variations
- Model Reduction and Neural Networks
- Neural Networks and Reservoir Computing
- RNA modifications and cancer
- Biomedical Text Mining and Ontologies
- Topic Modeling
Drexel University
2020-2025
University of California, Santa Barbara
2019-2020
Philadelphia University
2020
University of Chicago
2014-2019
Division of Materials Research
2019
University of Wisconsin–Madison
2012
Cornell University
2011
The self-assembly of block polymers into well-ordered nanostructures underpins their utility across fundamental and applied polymer science, yet only a handful equilibrium morphologies are known with the simplest AB-type materials. Here, we report discovery A15 sphere phase in single-component diblock copolymer melts comprising poly(dodecyl acrylate)-block-poly(lactide). A systematic exploration space revealed that forms substantial range minority lactide volume fractions (fL = 0.25 - 0.33)...
The interaction of DNA with proteins occurs over a wide range length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature plays significant role protein-binding properties. this work, we present coarse grained model is capable describing base-pairing, hybridization, major minor groove widths, curvature. represents an extension recently proposed 3SPN.2 description [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, de...
Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety methods exist in literature that can enhance considerably, increasingly sophisticated, effective algorithms continue to be developed at rapid pace. Implementation these techniques, however, challenging experts non-experts alike. There is clear need...
Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and mechanisms that dictate their position at specific locations along a DNA sequence are central importance to genetics. In this Letter, we employ molecular models proteins elucidate various aspects nucleosome positioning. particular, show how DNA's histone affinity is encoded its sequence-dependent shape, including subtle deviations from ideal straight B-DNA form local variations minor groove width. By relying on...
Nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism genetic regulation. Quantifying strength interactions nucleosome is a central problem in biophysics critical to understanding how positions influence gene expression. By comparing single-molecule experiments, we demonstrate that coarse-grained molecular model can reproduce key aspects unwrapping. Using detailed simulations DNA histone proteins,...
Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations nucleosomes across genome not random but instead depend on both underlying DNA sequence dynamic action other proteins within nucleus. These central to function, molecular details interplay between nucleosome dynamics remain poorly understood. In this work, we investigate in detail relying a model, permits development comprehensive picture...
The grafting-through copolymerization of two distinct macromonomers via ring-opening metathesis polymerization is typically used to form statistical or diblock bottlebrush polymers with large total backbone degrees (NBB) relative that the side-chains (NSC). Here, we demonstrate Grubbs-type chemistry in opposite limit, namely NBB ≪ NSC, produces well-defined materials excellent control over ensemble-averaged properties, including molar mass, dispersity, composition, and number branch points....
Protein A chromatography is typically used as the initial capture step in purification of monoclonal antibodies produced Chinese hamster ovary (CHO) cells. Although exploiting an affinity interaction for purification, level host cell proteins protein eluent varies significantly with different feedstocks. Using a batch binding method, we performed controlled study to assess clearance across both MabSelect Sure and Prosep vA resins. We individually spiked 21 purified into null culture fluid...
A recently published coarse-grained DNA model [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and de Pablo, Chem. Phys. 139, 144903 (2013)] is used to study the hybridization mechanism of oligomers. Forward flux sampling construct ensembles reactive trajectories from which effects sequence, length, ionic strength are revealed. Heterogeneous sequences observed hybridize via canonical zippering mechanism. In contrast, homogeneous through a slithering mechanism, while more complex base pair...
The supramolecular chromatin fiber is governed by molecular scale energetics and interactions. Such originate from the fiber's building block, nucleosome core particle (NCP). In recent years, has been examined through perturbative methods in attempts to extract of association fiber. This body work led different results experiments simulations concerning nucleosome-nucleosome energetics. Here, we expand on previous use coarse-grained evaluate inherent nucleosomes across a variety parameters...
Asymmetric miktoarm star polymers produce unique material properties, yet existing synthetic strategies are beleaguered by complicated reaction schemes restricted in both the monomer scope and yield. Here, we introduce a new approach coined "μSTAR", synthesis termination after ring-opening metathesis polymerization, that circumvents these traditional limitations constructing block–block junction scalable one-pot process involving (1) grafting-through polymerization of macromonomer followed...
A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, this manifested gene expression. The wide range length scales that genome presents important challenges; epigenetic to histones occur on angstroms, yet resulting effects these can span micrometers. There a scarcity computational tools capable providing mechanistic picture molecular information from individual propagated up large regions genome. In work, new model...
It is difficult to quantify structure-property relationships and identify structural features of complex materials. The characterization amorphous materials especially challenging because their lack long-range order makes it define metrics. In this work, we apply deep learning algorithms accurately classify characterize features. Specifically, show that convolutional neural networks message passing can two-dimensional liquids liquid-cooled glasses from molecular dynamics simulations with...
In this study, we use self-consistent field theory to demonstrate that the A(BA′)n miktoarm architecture can strongly deflect order–order phase boundaries large volume fractions fA. The achieves strong deflection by combining effects of frustration and block bidispersity is shown stabilize discrete spheres cylinders A up values fA = 0.58 0.78, respectively. We next analyze prevalence chain bridging νB in both neat melts homopolymer blends form fluctuation-stabilized "bricks mortar" phase....
Bottlebrush block polymers are a promising platform for self-assembled photonic materials, yet most work has been limited to one-dimensional crystals based on the lamellar phase. Here we demonstrate with simulation that nonfrustrated ABC bottlebrush can be used self-assemble three-dimensional complete band gaps. To show this, have developed computational approach couples self-consistent field theory (SCFT) simulations Maxwell's equations, thereby permitting direct link between molecular...
Molecular architecture plays a key role in the self-assembly of block copolymers, but few studies have systematically examined influence chain connectivity on tetrahedrally close-packed (TCP) sphere phases. Here, we report versatile material platform comprising two blocks with substantial conformational asymmetry, A = poly(trifluoroethyl acrylate) and B poly(dodecyl acrylate), use it to compare phase behavior AB diblocks, ABA triblocks, (AB)n radial star copolymers n 3 or 4. Each forms TCP...
Particle-based and field-theoretic simulations are both widely used methods to predict the properties of polymeric materials. In general, advantages each method complementary. Field-theoretic preferred for polymers with high molecular weights can provide direct access chemical potentials free energies, which makes them method-of-choice calculating phase diagrams. The trade-off is that sacrifice details present in particle-based simulations, such as configurations individual molecules their...
Reaction-induced phase transitions use chemical reactions to drive macromolecular organisation and self-assembly. This review highlights significant recent advancements in this burgeoning field.
Particle and field-theoretic simulations are both commonly used methods to study the equilibrium properties of polymeric materials. Yet despite formal equivalence two methods, no comprehensive comparisons particle exist in literature. In this work, we seek fill gap by performing a systematic quantitative comparison simulations. our comparison, consider four representative systems: homopolymer melt/solution, diblock copolymer melt, polyampholyte solution, polyelectrolyte gel. For each these...
Insulin, the primary hormone regulating level of glucose in bloodstream, modulates a variety cellular and enzymatic processes normal diseased cells. Insulin signals are processed by complex network biochemical interactions which ultimately induce gene expression programs or other such as translation initiation. Surprisingly, despite wealth literature on insulin signaling, relative importance components linking with initiation remains unclear. We addressed this question developing...
The emerging field of materials informatics has the potential to greatly reduce time-to-market and development costs for new materials. success such efforts hinges on access large, high-quality databases material properties. However, many data are only be found encoded in text within esoteric scientific articles, a situation that makes automated extraction difficult manual time-consuming error-prone. To address this challenge, we present hybrid Information Extraction (IE) pipeline improve...
The self-assembly of DNA-conjugated nanoparticles represents a promising avenue toward the design engineered hierarchical materials. By using DNA to encode nanoscale interactions, macroscale crystals can be formed with mechanical properties that can, at least in principle, tuned. Here we present silico evidence response these assemblies indeed controlled, and subtle modifications linking sequences change Young's modulus from 97 kPa 2.1 MPa. We rely on detailed molecular model quantify...
Nanoparticles functionalized with short sequences of DNA represent a promising platform for customizable self assembly. Though much recent research has focused on the phase behavior and assembly these structures, little been done to precisely characterize pairwise interaction between particles. Here we present detailed calculation association DNA-nanoparticle conjugates using 3SPN.2, coarse-grained model that accounts molecular structure base-pairing. We compare our results those obtained...