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Publications

A computationally efficacious free-energy functional for studies of inhomogeneous liquid water.

Cornell Affiliated Author(s)
Author
R. Sundararaman
K. Letchworth-Weaver
Tomas Arias
Abstract

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.

Journal
The Journal of chemical physics
Date Published
Group (Lab)
Tomas Arias Group

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

Cornell Affiliated Author(s)
Author
S. Boutet
L. Lomb
G.J. Williams
T.R.M. Barends
A. Aquila
R.B. Doak
U. Weierstall
D.P. DePonte
J. Steinbrener
R.L. Shoeman
M. Messerschmidt
A. Barty
T.A. White
S. Kassemeyer
R.A. Kirian
M.M. Seibert
P.A. Montanez
C. Kenney
R. Herbst
P. Hart
J. Pines
G. Haller
Sol Gruner
H.T. Philipp
M.W. Tate
M. Hromalik
L.J. Koerner
N. Van Bakel
J. Morse
W. Ghonsalves
D. Arnlund
M.J. Bogan
C. Caleman
R. Fromme
C.Y. Hampton
M.S. Hunter
L.C. Johansson
G. Katona
C. Kupitz
M. Liang
A.V. Martin
K. Nass
L. Redecke
F. Stellato
N. Timneanu
D. Wang
N.A. Zatsepin
D. Schafer
J. Defever
R. Neutze
P. Fromme
J.C.H. Spence
H.N. Chapman
I. Schlichting
Abstract

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.

Journal
Science
Date Published
Research Area
Group (Lab)
Sol M. Gruner Group

Adaptive temperature compensation in circadian oscillations

Cornell Affiliated Author(s)
Author
P. François
N. Despierre
E.D. Siggia
Abstract

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.

Journal
PLoS Computational Biology
Date Published
Research Area

Dynamics of TGF-β signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4

Cornell Affiliated Author(s)
Author
A. Warmflash
Q. Zhang
B. Sorre
A. Vonic
E.D. Siggia
A.H. Brivanlou
Abstract

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.

Journal
Proceedings of the National Academy of Sciences of the United States of America
Date Published
Funding Source
R01HD032105
Research Area

Dual-detector X-ray fluorescence imaging of ancient artifacts with surface relief

Cornell Affiliated Author(s)
Author
D.-M. Smilgies
J.A. Powers
D.H. Bilderback
R.E. Thorne
Abstract

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.

Journal
Journal of Synchrotron Radiation
Date Published
Group (Lab)
Robert Thorne Group

Evaluating metacognitive scaffolding in Guided Invention Activities

Cornell Affiliated Author(s)
Author
I. Roll
N.G. Holmes
J. Day
D. Bonn
Abstract

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.

Journal
Instructional Science
Date Published
Funding Source
-0836012
Group (Lab)
Natasha Holmes Group

Protein crowding impedes pressure-induced unfolding of staphylococcal nuclease

Cornell Affiliated Author(s)
Author
S. Wang
M.W. Tate
Sol Gruner
Abstract

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.

Journal
Biochimica et Biophysica Acta - General Subjects
Date Published
Funding Source
DMR-0225180
DEFG02-97ER62443
Research Area
Group (Lab)
Sol M. Gruner Group

Small machines

Cornell Affiliated Author(s)
Author
P.L. McEuen
Abstract

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.

Journal
Daedalus
Date Published
Group (Lab)
Paul McEuen Group

Visualization of the emergence of the pseudogap state and the evolution to superconductivity in a lightly hole-doped Mott insulator

Cornell Affiliated Author(s)
Author
Y. Kohsaka
T. Hanaguri
M. Azuma
M. Takano
J.C. Davis
H. Takagi
Abstract

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.

Journal
Nature Physics
Date Published
Group (Lab)
J.C. Seamus Davis Group

Temperature dependence of the electronic structure and Fermi-surface reconstruction of Eu 1-xGd xO through the ferromagnetic metal-insulator transition

Cornell Affiliated Author(s)
Author
D.E. Shai
A.J. Melville
J.W. Harter
E.J. Monkman
D.W. Shen
A. Schmehl
D.G. Schlom
K.M. Shen
Abstract

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.

Journal
Physical Review Letters
Date Published
Group (Lab)
Kyle Shen Group