Bojan Zagrovic, Guha Jayach, Ian S. Millett, Sebastian Doniach, Vijay S. P
Using synchrotron radiation and the small-angle X-ray scattering technique we have measured the radii of gyration of a series of alaninebased a-helix-forming peptides of the composition Ace-(AAKAA)...
Josephson current in graphene: the role of unconventional pairing symmetries (2009)
Linder, Jacob, Black-Schaffer, Annica M., Yokoyama, Takehito, Doniach, Sebastian, Sudbø, Asle
We investigate the Josephson current in a graphene superconductor/normal/superconductor junction, where superconductivity is induced by means of the proximity effect from external contacts. We take...
Black-Schaffer, Annica M., Doniach, Sebastian
While not widely recognized, electronic correlations might play an important role in graphene. Indeed, Pauling's resonance valence bond (RVB) theory for the pp-bonded planar organic molecules, of...
Black-Schaffer, Annica M., Doniach, Sebastian
Using the self-consistent tight-binding Bogoliubov-de Gennes formalism we have studied the effect of nearest neighbor spin-singlet bond (SB) correlations on Josephson coupling and proximity effect in...
Wenjun Zheng, Adviser Prof, Sebastian Doniach
Seeking challenging research and teaching position in computational molecular biology and theoretical biophysics at major universities or research institutes.
Black-Schaffer, Annica M., Doniach, Sebastian
We use a tight-binding Bogoliubov-de Gennes (BdG) formalism to self-consistently calculate the proximity effect, Josephson current, and local density of states in ballistic graphene SNS Josephson...
Franklin, Joel, Koehl, Patrice, Doniach, Sebastian, Delarue, Marc
The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an...
Resonating valence bonds and mean-field d-wave superconductivity in graphite (2006)
Black-Schaffer, Annica M., Doniach, Sebastian
We investigate the possibility of inducing superconductivity in a graphite layer by electronic correlation effects. We use a phenomenological microscopic Hamiltonian which includes nearest neighbor...
Columbus, Linda, Lipfert, Jan, Klock, Heath, Millett, Ian, Doniach, Sebastian, Lesley, Scott A.
Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be...
Columbus, Linda, Lipfert, Jan, Klock, Heath, Millett, Ian, Doniach, Sebastian, Lesley, Scott A.
Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be...
Columbus, Linda, Lipfert, Jan, Klock, Heath, Millett, Ian, Doniach, Sebastian, Lesley, Scott A.
Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be...
Fold recognition aided by constraints from small angle X-ray scattering data (2005)
Zheng, Wenjun, Doniach, Sebastian
We performed a systematic exploration of the use of structural information derived from small angle X-ray scattering (SAXS) measurements to improve fold recognition. SAXS data provide the Fourier...
Fold recognition aided by constraints from small angle X-ray scattering data (2005)
Zheng, Wenjun, Doniach, Sebastian
We performed a systematic exploration of the use of structural information derived from small angle X-ray scattering (SAXS) measurements to improve fold recognition. SAXS data provide the Fourier...
Computer Simulation of Protein-Protein and Protein-Peptide Interactions. (1998)
A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work...
Association-induced folding of globular proteins
Uversky, Vladimir N., Segel, Daniel J., Doniach, Sebastian, Fink, Anthony L.
It has generally been assumed that the aggregation of partially folded intermediates during protein refolding results in the termination of further protein folding. We show here, however, that under...
Exploring the folding landscape of a structured RNA
Russell, Rick, Zhuang, Xiaowei, Babcock, Hazen P., Millett, Ian S., Doniach, Sebastian, Chu, Steven, ...
Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach:...
Rapid compaction during RNA folding
Russell, Rick, Millett, Ian S., Tate, Mark W., Kwok, Lisa W., Nakatani, Bradley, Gruner, Sol M., ...
We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a...
A comparative study of motor-protein motions by using a simple elastic-network model
Zheng, Wenjun, Doniach, Sebastian
In this work, we report on a study of the structure-function relationships for three families of motor proteins, including kinesins, myosins, and F1-ATPases, by using a version of the simple...
Random-coil behavior and the dimensions of chemically unfolded proteins
Kohn, Jonathan E., Millett, Ian S., Jacob, Jaby, Zagrovic, Bojan, Dillon, Thomas M., Cingel, Nikolina, ...
Spectroscopic studies have identified a number of proteins that appear to retain significant residual structure under even strongly denaturing conditions. Intrinsic viscosity, hydrodynamic radii, and...
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
Bai, Yu, Das, Rhiju, Millett, Ian S., Herschlag, Daniel, Doniach, Sebastian
Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion...
Unusual compactness of a polyproline type II structure
Zagrovic, Bojan, Lipfert, Jan, Sorin, Eric J., Millett, Ian S., Van Gunsteren, Wilfred F., Doniach, Sebastian, ...
Polyproline type II (PPII) helix has emerged recently as the dominant paradigm for describing the conformation of unfolded polypeptides. However, most experimental observables used to characterize...
Association-induced folding of globular proteins
Uversky, Vladimir N., Segel, Daniel J., Doniach, Sebastian, Fink, Anthony L.
It has generally been assumed that the aggregation of partially folded intermediates during protein refolding results in the termination of further protein folding. We show here, however, that under...
Exploring the folding landscape of a structured RNA
Russell, Rick, Zhuang, Xiaowei, Babcock, Hazen P., Millett, Ian S., Doniach, Sebastian, Chu, Steven, ...
Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach:...
Rapid compaction during RNA folding
Russell, Rick, Millett, Ian S., Tate, Mark W., Kwok, Lisa W., Nakatani, Bradley, Gruner, Sol M., ...
We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a...
A comparative study of motor-protein motions by using a simple elastic-network model
Zheng, Wenjun, Doniach, Sebastian
In this work, we report on a study of the structure-function relationships for three families of motor proteins, including kinesins, myosins, and F1-ATPases, by using a version of the simple...
Random-coil behavior and the dimensions of chemically unfolded proteins
Kohn, Jonathan E., Millett, Ian S., Jacob, Jaby, Zagrovic, Bojan, Dillon, Thomas M., Cingel, Nikolina, ...
Spectroscopic studies have identified a number of proteins that appear to retain significant residual structure under even strongly denaturing conditions. Intrinsic viscosity, hydrodynamic radii, and...
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
Bai, Yu, Das, Rhiju, Millett, Ian S., Herschlag, Daniel, Doniach, Sebastian
Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion...
Unusual compactness of a polyproline type II structure
Zagrovic, Bojan, Lipfert, Jan, Sorin, Eric J., Millett, Ian S., Van Gunsteren, Wilfred F., Doniach, Sebastian, ...
Polyproline type II (PPII) helix has emerged recently as the dominant paradigm for describing the conformation of unfolded polypeptides. However, most experimental observables used to characterize...
Franklin, Joel, Koehl, Patrice, Doniach, Sebastian, Delarue, Marc
The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an...
Columbus, Linda, Lipfert, Jan, Klock, Heath, Millett, Ian, Doniach, Sebastian, Lesley, Scott A.
Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be...
Evaluation of Ion Binding to DNA Duplexes Using a Size-Modified Poisson-Boltzmann Theory
Chu, Vincent B., Bai, Yu, Lipfert, Jan, Herschlag, Daniel, Doniach, Sebastian
Poisson-Boltzmann (PB) theory is among the most widely applied electrostatic theories in biological and chemical science. Despite its reasonable success in explaining a wide variety of phenomena, it...
Dynamic charge interactions create surprising rigidity in the ER/K α-helical protein motif
Sivaramakrishnan, Sivaraj, Spink, Benjamin J., Sim, Adelene Y. L., Doniach, Sebastian, Spudich, James A.
Protein α-helices are ubiquitous secondary structural elements, seldom considered to be stable without tertiary contacts. However, amino acid sequences in proteins that are based on alternating...