Publications
A computationally efficacious free-energy functional for studies of inhomogeneous liquid water.
We present an accurate equation of state for water based on a simple microscopic Hamiltonian, with only four parameters that are well-constrained by bulk experimental data. With one additional parameter for the range of interaction, this model yields a computationally efficient free-energy functional for inhomogeneous water, which captures short-ranged correlations, cavitation energies, and, with suitable long-range corrections, the nonlinear dielectric response of water, making it an excellent candidate for the studies of mesoscale water and for use in ab initio solvation methods.
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography
Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme.
Adaptive temperature compensation in circadian oscillations
A temperature independent period and temperature entrainment are two defining features of circadian oscillators. A default model of distributed temperature compensation satisfies these basic facts yet is not easily reconciled with other properties of circadian clocks, such as many mutants with altered but temperature compensated periods. The default model also suggests that the shape of the circadian limit cycle and the associated phase response curves (PRC) will vary since the average concentrations of clock proteins change with temperature.
Dynamics of TGF-β signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4
The TGF-β pathway plays a vital role in development and disease and regulates transcription through a complex composed of receptor-regulated Smads (R-Smads) and Smad4. Extensive biochemical and genetic studies argue that the pathway is activated through R-Smad phosphorylation; however, the dynamics of signaling remain largely unexplored. We monitored signaling and transcriptional dynamics and found that although R-Smads stably translocate to the nucleus under continuous pathway stimulation, transcription of direct targets is transient.
Dual-detector X-ray fluorescence imaging of ancient artifacts with surface relief
Interpretation of X-ray fluorescence images of archeological artifacts is complicated by the presence of surface relief and roughness. Using two symmetrically arranged fluorescence detectors in a back-reflection geometry, the proper X-ray fluorescence yield can be distinguished from intensity variations caused by surface topography. This technique has been applied to the study of Roman inscriptions on marble. © 2012 International Union of Crystallography.
Evaluating metacognitive scaffolding in Guided Invention Activities
Invention and Productive Failure activities ask students to generate methods that capture the important properties of some given data (e. g., uncertainty) before being taught the expert solution. Invention and Productive Failure activities are a class of scientific inquiry activities in that students create, implement, and evaluate mathematical models based on data. Yet, lacking sufficient inquiry skills, students often do not actualize the full potential of these activities.
Protein crowding impedes pressure-induced unfolding of staphylococcal nuclease
Background: In the cellular environment, macromolecules occupy about 30% of a cell's volume. In this crowded environment, proteins behave very differently than in dilute solution where scientists typically study the properties of proteins. For this reason, recent studies have investigated proteins in cell-like crowded conditions so as to understand if this changes their properties. The present study was performed to examine if molecular crowding impedes the protein unfolding process that is known to occur upon the application of high pressure.
Small machines
Over the last fifty years, small has emerged as the new big thing. The reduction of information and electronics to nanometer dimensions has revolutionized science, technology, and society. Now scientists and engineers are creating physical machines that operate at the nanoscale. Using approaches ranging from lithographic patterning to the co-opting of biological machinery, new devices are being built that can navigate, sense, and alter the nanoscale world.
Visualization of the emergence of the pseudogap state and the evolution to superconductivity in a lightly hole-doped Mott insulator
Superconductivity emerges from the cuprate antiferromagnetic Mott state with hole doping. The resulting electronic structure is not understood, although changes in the state of oxygen atoms seem paramount. Hole doping first destroys the Mott state, yielding a weak insulator where electrons localize only at low temperatures without a full energy gap. At higher doping levels, the ' pseudogap', a weakly conducting state with an anisotropic energy gap and intra-unit-cell breaking of 90 ° rotational (C 4v) symmetry, appears.
Temperature dependence of the electronic structure and Fermi-surface reconstruction of Eu 1-xGd xO through the ferromagnetic metal-insulator transition
We present angle-resolved photoemission spectroscopy of Eu 1-xGd xO through the ferromagnetic metal-insulator transition. In the ferromagnetic phase, we observe Fermi surface pockets at the Brillouin zone boundary, consistent with density functional theory, which predicts a half-metal. Upon warming into the paramagnetic state, our results reveal a strong momentum-dependent evolution of the electronic structure, where the metallic states at the zone boundary are replaced by pseudogapped states at the Brillouin zone center due to the absence of magnetic long-range order of the Eu 4f moments.