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The Link lab has used bioinformatic techniques to find a new class of lasso peptides in water-dwelling bacteria. A characteristic of the gene clusters that encode these lasso peptides is a gene encoding a lasso peptide isopeptidase, which recognizes the knotted structure of a lasso peptide and cleaves it into a linear peptide.
Catenanes are interlocked molecules in which constituents are held together by mechanical bonds rather than covalent bonds. A catenane with 3 interlocking rings (a [3]catenane) was built by enzymatically cleaving a variant of the lasso peptide microcin J25. The cleaved peptides self-assembled into the [3]catenane shown here, the structure of which was determined by NMR.
New permselective polymeric materials to enable the recovery and concentration of butanol from dilute aqueous solution, such as fermentation broth have been developed. Energy-efficient recovery of butanol is an essential enabling technology for the large-scale production of butanol as both a chemical building block, and eventually, biofuel.
A new technique uses nonlinear manifold learning to infer structural relationships between colloidal particles based on their local topology. This approach facilitates the identification of crystal structures during self-assembly, when they may be distorted, defective, or even unknown.
Changing from a linear to a star block copolymer architecture can yield substantial improvements in the properties of thermoplastic elastomers (TPEs), such as their tensile strength and recovery from deformation. TPEs are melt-processable, reprocessable and recyclable, but typically show incomplete recovery from deformation when compared with conventional vulcanized elastomers.
Electrochromic window technologies offer dynamic control of the optical transmission of the visible and near-IR portions of the solar spectrum to reduce lighting, heating and cooling needs. Solar cells harvesting near-UV photons could satisfy the unmet need of powering such smart windows without competing for visible or near-IR photons and without aesthetic and design constraints.
Drying colloidal mixtures can undergo a spontaneous, nonequilibrium vertical separation into layers enriched in particles of a specific size, an effect which can be exploited to create functional coatings. Using simulations, we showed how the size of these layers depends on the particle size ratio and the drying rate, and proposed a model based on dynamical density functional theory to explain the observed phenomena.
Mechanical deformations endured by flexible electronics can induce changes in the electrical resistance of their active electronic component. This effect is quantified by a parameter called the gauge factor. The tunability of both the polarity and the magnitude of the gauge factor of electrically conducting polyaniline can be achieved by structural manipulation.
Ductal carcinoma in situ (DCIS) accounts for 20% of all breast cancer diagnoses in the United States. Graduate student Eline Boghaer used lattice-based computational modeling to explore the progression between classes of DCIS.
Prof. Brynildsen is a recipient of an NSF CAREER award that focuses on studying nitric oxide stress in bacteria with approaches adopted from metabolic engineering to discover novel antivirulence therapies. Depicted above, a simplified diagram of the Escherichia coli nitric oxide response network.
The size of a typical eukaryotic cell is usually of the order of ~10 μm. However, some cell types grow to very large sizes, up to 1 mm. Graduate student Marina Feric in the Brangwynne lab has used microrheology and quantitative imaging to show that large nuclei contain an elastic F-actin scaffold that mechanically stabilizes them against gravitational forces.
Grad student Mikhail Maksimov *15 and Professor Jamie Link have isolated and characterized an enzyme, lasso peptide isopeptidase, that “unties” the lasso structure. This enzyme suggests additional layers of regulation or perhaps new functions for lasso peptides.
Professor Jamie Link and grad student Frank Piscotta, in collaboration with the Liu group at Texas A&M, have provided the first demonstration that unnatural amino acids can be introduced into the antimicrobial lasso peptide microcin J25. Four different amino acids were tolerated at four different positions, and all 16 of these variants retained antimicrobial activity.
Small molecules – be they pharmaceuticals, explosives, dyes, flavors for food, or, as the Loo Group studies, molecular semiconductors – can adopt a variety of crystal structures, a phenomenon known as polymorphism.
Grain boundaries act as bottlenecks to charge transport in organic field effect transistors comprising polycrystalline active areas. In the Loo Lab, we have found that the impact of these boundaries depends on the structure of the organic semiconductor (molecular or polymeric) and the method of thin-film formation (solution-processing or thermal evaporation).
Computer simulations suggest that pure photonic crystals could be created from a mixture in which colloidal particles are dispersed in a polymer melt.
Computer simulations can be used to explore what happens to water as it is cooled to temperatures below freezing. A recent study found that the supercooled liquid separates into two liquids with different densities.
An NSF award by the Office of Emerging Frontiers in Research and Innovation supports work designed to address a fundamental question of developmental biology: what controls the spatial and temporal patterns of cell differentiation?
A simple lattice model of prochiral reactants, chiral products and inert solvent was formulated to study the kinetics of chiral symmetry breaking via asymmetric autocatalysis and inhibition, which have been proposed as key processes in the spontaneous emergence of chiral symmetry breaking in a prebiotic world.
Block copolymer nanoparticles undergo rapid thermal cycling in a polymerase chain reaction (PCR), including temperatures that reach as high as 95 °C. The high temperature treatment causes the nanoparticles to disassemble since the core of the particles is held together only by non-covalent forces.
A photo of the scintillator vessel and shroud inside Borexino Solar Neutrino Detector at Gran Sasso in Italy. The detector consists of nested nylon vessels fabricated at Princeton that hold liquid scintillator.
A comparison of the ignition front dynamics for co-current and counter-current flow of hydrogen and oxygen in a Parallel Flow Channel PEM fuel cell. The color scale is for the local current density as a function of the axial position from the hydrogen inlet.
Molecular simulation illustrating the mechanisms of failure of thin films of amorphous solid water in nano-scale confinement.
Microcin J25 is a small 21-residue antimicrobial peptide exhibiting an interesting "lasso" motif whereby the N-terminal glycine 1 is covalently bonded via a peptide bond to the glutamic acid 8 sidechain to form a loop through which the C-terminus is threaded and sterically locked in place by bulky aromatic groups either side of the ring.
Color map of the orientation adopted by a sphere-forming block copolymer thin film following two sequential rotational shearing operations.
Isolated n-alkane chains in water serve as useful model systems in which to study the role of hydrophobicity in protein folding.
The channel region of solution-processed organic thin film transistors using triethylsilylethynyl anthradithiophene (TES-ADT)as the organic semiconductor. Grain size is controlled by the addition of fluorinated-TES-ADT, which acts as heterogeneous nuclei for TES-ADT crystallization.
Isolated n-alkane chains in water serve as useful model systems in which to study the role of hydrophobicity in protein folding. A nonlinear dimensionality reduction technique known as the diffusion map, was applied to long molecular dynamics simulations of n-alkane chains to systematically extract order parameters describing the slow, fundamental dynamics of the chain.
An example of nanofabrication through the replication of a block copolymer thin film template. Top portion of the image shows an array of gold dots, 30 nm diameter and 18 nm thick, on a silicon wafer substrate. The lower potion shows the mask through which these dots were deposited: a 10 nm-thick silicon nitride membrane, perforated with holes of 30 nm diameter.
Two-dimensional small-angle x-ray scattering patterns reveal the nanostructure of two styrene-diene-styrene triblock copolymers which have been aligned through channel die compression. Left: a lamella-forming triblock showing a biaxial texture (four-spot pattern). Right: a cylinder-forming triblock showing a single-crystal texture (six-spot pattern).
A comparison of the local current density for co-current and counter-current flow of hydrogen and oxygen in a segmented anode PEM fuel cell. Current ignition is indicated by a jump in the current from near zero to ~ 100mA.The top two are the experimental currents for co-current flows (left) and counter-current flows (right). The bottom two are reaction-diffusion model simulations.
Crystal structures of spherical colloids: [i] binary mixture of large and small spheres, [ii] colloids in an external electric field, and [ii] binary mixture of oppositely charged colloids.
The Shvartsman lab studies mechanical properties of developing tissues. The image shows a developing Drosophila egg, which is surrounded by a simple columnar epithelium. The layer is composed of two kinds of cells - normal (with green nuclei) and mutant. Such heterogeneities, which can be robustly generated using techniques of Drosophila genetics, can be used to systematically test the cellular and continuum mechanics descriptions of developing tissues.
Rotational trajectory of a unit vector on a model molecule representing the glass-forming substance ortho-terphenyl. This computer simulation illustrates the progressive slowing down of rotational motion upon cooling, which occurs as molecules become trapped in a transient cage of immobile neighbors.
This is a top-view of a thin-film transistor, the basic building block for integrated circuits. The source and drain interdigitated electrodes of this transistor consist of a conductive polymer, polyaniline, that is directly patternable from an aqueous dispersion. Its active component (green rectangle) is pentacene, an organic semiconductor.
X-ray diffraction pattern from a newly-synthesized diblock copolymer containing a linear (high-density) polyethylene block. As designed, the material self-assembles into a lamellar nanostructure, with layers of polyethylene alternating with layers of glassy polyvinylcyclohexane. Macroscopic alignment of the structure was achieved by planar extensional flow in a lubrication channel die.