115 research outputs found
Documentation of the GLAS fourth order general circulation model. Volume 1: Model documentation
The volume 1, of a 3 volume technical memoranda which contains a documentation of the GLAS Fourth Order General Circulation Model is presented. Volume 1 contains the documentation, description of the stratospheric/tropospheric extension, user's guide, climatological boundary data, and some climate simulation studies
Documentation of the GLAS fourth order general circulation model. Volume 2: Scalar code
Volume 2, of a 3 volume technical memoranda contains a detailed documentation of the GLAS fourth order general circulation model. Volume 2 contains the CYBER 205 scalar and vector codes of the model, list of variables, and cross references. A variable name dictionary for the scalar code, and code listings are outlined
Documentation of the GLAS fourth order general calculation model. Volume 3: Vectorized code for the Cyber 205
Volume 3 of a 3-volume technical memoranda which contains documentation of the GLAS fourth order genera circulation model is presented. The volume contains the CYBER 205 scalar and vector codes of the model, list of variables, and cross references. A dictionary of FORTRAN variables used in the Scalar Version, and listings of the FORTRAN Code compiled with the C-option, are included. Cross reference maps of local variables are included for each subroutine
Folding and insertion thermodynamics of the transmembrane WALP peptide
The anchor of most integral membrane proteins consists of one or several
helices spanning the lipid bilayer. The WALP peptide, GWW(LA)(L)WWA, is a
common model helix to study the fundamentals of protein insertion and folding,
as well as helix-helix association in the membrane. Its structural properties
have been illuminated in a large number of experimental and simulation studies.
In this combined coarse-grained and atomistic simulation study, we probe the
thermodynamics of a single WALP peptide, focusing on both the insertion across
the water-membrane interface, as well as folding in both water and a membrane.
The potential of mean force characterizing the peptide's insertion into the
membrane shows qualitatively similar behavior across peptides and three force
fields. However, the Martini force field exhibits a pronounced secondary
minimum for an adsorbed interfacial state, which may even become the global
minimum---in contrast to both atomistic simulations and the alternative PLUM
force field. Even though the two coarse-grained models reproduce the free
energy of insertion of individual amino acids side chains, they both
underestimate its corresponding value for the full peptide (as compared with
atomistic simulations), hinting at cooperative physics beyond the residue
level. Folding of WALP in the two environments indicates the helix as the most
stable structure, though with different relative stabilities and chain-length
dependence.Comment: 12 pages, 5 figure
Stratospheric Data Analysis System (STRATAN)
A state of the art stratospheric analyses using a coupled stratosphere/troposphere data assimilation system is produced. These analyses can be applied to stratospheric studies of all types. Of importance to this effort is the application of the Stratospheric Data Analysis System (STRATAN) to constituent transport and chemistry problems
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Direct Evidence for Aligned Binding of Cellulase Enzymes to Cellulose Surfaces
The conversion of biomass into green fuels and chemicals is of great societal interest. Engineers have been designing new cellulase enzymes for the breakdown of otherwise insoluble cellulose materials. A barrier to the rational design of new enzymes has been our lack of a molecular picture of how cellulase binding occurs. A critical factor is the attachment via the enzyme’s carbohydrate binding module (CBM). To elucidate the structural and mechanistic details of cellulase adsorption, we have combined experimental data from sum frequency generation spectroscopy with molecular dynamics simulations to probe the equilibrium structure and surface alignment of a 14-residue peptide mimicking the CBM. The data show that binding is driven by hydrogen bonding and that tyrosine side chains within the CBM align the cellulase with the registry of the cellulose surface. Such an alignment is favorable for the translocation and effective cellulose breakdown and is therefore likely an important parameter for the design of novel enzymes.
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