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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.
ASTRO-FOLD, a first principles method for protein structure prediction, is based on an overall deterministic global optimization framework (αBB) coupled with a stochastic algorithm, conformational space annealing (CSA).
We have developed a new computational framework to fully characterize the three-dimensional porous structure of zeolites, microporous aluminosilicate crystals used in catalysis and separations.
The United States transportation sector's dependence on petroleum has motivated efforts to discover alternative energy sources and processes to fulfill the nation's demand. A novel hybrid coal, biomass, and natural gas to liquid (CBGTL) process has been developed to produce gasoline, diesel, and kerosene in ratios consistent with the United States transportation demands.
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.
Using tandem mass spectrometry and mixed-integer linear optimization, a comprehensive list of proteins along with their corresponding post-translational modifications can be derived. Given a mixture of unknown proteins that may be post-translationally modified, liquid chromatography and tandem mass spectrometry (LC-MS/MS) is used to separate, ionize, and fragment the digested peptides from the mixture.
De novo protein design seeks to determine the amino acid sequence or sequences that will fold into a given 3-dimensional template. One application of protein design is to discover novel peptide sequences that will bind with greater affinity than the native sequence to a target protein. Many computational tools are utilized to achieve this desired result.
The pooling problem is a challenge seeking to maximize profit subject to feedstock availability, intermediate storage capacity, demand, and product specifications on a network of interconnected nodes. We have extended the pooling problem to incorporate the Environmental Protection Agency's Complex Emissions Model into the constraint set so that the final products comply with United States reformulated gasoline standards.
We propose a novel intertwined hybrid approach that exploits synergies among exact and metaheuristic algorithms to solve efficiently various Routing problems. The overall approach is exact, that is, it maintains the theoretical guarantee of reaching an optimal solution, but relies heavily on problem-specific heuristic components to accelerate the search.
The PILOT_PTM algorithm is designed to search the universe of post-translational modifications and annotate a peptide sequence with the modifications that best explain the experimental data. The overall framework for PILOT_PTM consists initially of the identification of globally and locally significant peaks. The highest intensity filtered peaks are labeled as globally significant.
The locations of hybrid coal, biomass, and natural gas to liquid (CBGTL) plants are dependent on (i) the locations and availabilities of the three feedstocks, and (ii) the locations and amount of product demands. An optimal energy supply chain network that lays out the most strategic locations for the new CBGTL plants is obtained by solving a mixed integer linear optimization model.
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.
The NMR structure of the HIV-1 gp120-CD4-CCR5 complex was employed as the flexible design template for the de novo design of a gp 120 inhibitor by optimizing the residues of CCR5. The flexibility of the V3 loop of gp120 is modeled by overlaying other NMR structures for the loop on top of the original single complex structure.
The top-half of the figure illustrates the study of proteomics using tandem mass spectrometry. The bottom-half of the figure illustrates several of the applications for optimal methods that we have developed for clustering based on mixed-integer linear optimization (MILP).
The central goal of our research is to develop sophisticated, robust, and industrially relevant frameworks aimed at improving process efficiency and profitability.
This is a map of the extent of strain experienced by popular molecules when they go through the pores of a class of absorbent materials known as zeolites.
The protein folding problem is one of the most challenging and interesting problems in computational biology. The main aim is to predict the final three dimensional structure of the protein, given its amino acid sequence.
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.