Description: Sea surface temperatures (SSTs), reconstructed from two Globigerinoides ruber (white) morphotypes (G. ruber sensu stricto, (s.s.); G. ruber sensu lato, ( s.l.)) Mg/Ca and alkenones (UK'37) from core MD01-2390 from the tropical South China Sea (SCS) during the last deglaciation reveal a proxy-dependent discrepancy in the temporal pattern of the deglacial warming. Alkenone data suggest that the deglacial warming is punctuated by a decrease in temperature between not, vert, similar17 and 15 ka BP, corroborating previously published alkenone UK'37 SST records from the southern SCS. Within dating uncertainties, this cooling is coeval with the Heinrich Event 1 (H1) time interval in the North Atlantic region, underscoring the imprints of northern hemisphere forcing on tropical SCS ocean temperatures. The deglacial UK'37 SST minimum is also paralleled by a maximum in G. ruber morphotype-specific d18O. G. ruber Mg/Ca SST estimates suggest a morphotype-specific record of SSTs during the time interval of H1. Whereas G. ruber s.s. imply a continuous warming starting around 18 ka BP without any marked response to H1, G. ruber s.l.-based Mg/Ca SST estimates reveal a cooling around not, vert, similar17-15 ka BP similar to the H1 interval cooling seen in the alkenone SST record. Similar proxy-dependent differences in deglacial surface water warming have been recorded in the eastern equatorial Pacific, implying a common pattern on both sides of the tropical Pacific Ocean. We submit that this discrepancy could be due to differences in seasonality of planktonic foraminifera G. ruber morphotypes and alkenone-producing algae.

Description: Upper water column dynamics in the southern South China Sea were reconstructed in order to track changes in the activity of the East Asian winter monsoon (EAWM) since the Last Glacial Maximum. We used the difference in the stable oxygen isotopes (Delta d18O) and Mg/Ca-based temperatures (Delta T) of surface-dwelling (G. ruber) and thermocline-dwelling (P. obliquiloculata) planktonic foraminifera and the temperature difference between alkenone- and P. obliquiloculata Mg/Ca-based temperatures to estimate the upper ocean thermal gradient at International Marine Past Global Change Study (IMAGES) core MD01-2390. Estimates of the upper ocean thermal gradient were used to reconstruct mixed layer dynamics. We find that ourDelta d18O estimates are biased by changes in salinity and, thus, do not display a true upper ocean thermal gradient. The Delta T of G. ruber and P. obliquiloculata as well as the alkenone and P. obliquiloculata suggest increased surface water mixing during the late glacial, likely due to enhanced EAWM winds. Surface water mixing was weaker during the late Holocene, indicating a weaker influence of winter monsoon winds. The weakest winter monsoon activity occurred between 6.5 ka and 2.5 ka. Inferred EAWM changes since the Last Glacial Maximum coincide with EAWM changes as recorded in Chinese loess sediments. We find that the intensity of the EAWM and the East Asian summer monsoon show an inverse behavior during the last glacial and deglaciation but covaried during the middle to late Holocene.

Description: Background: With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results: Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions: The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano shapes in conjunction with biological macromolecule(s). Charges and radii on the macromolecule atoms and the atoms in the shapes are assigned according to the user's preferences allowing various scenarios of modeling. The default output file is in PQR (PQRE) format which is readable by almost any software available in biophysical field. It can be downloaded from: http://compbio.clemson.edu/downloadDir/ProNO_integrator.tar.gz

Description: Background: Accurate modeling of electrostatic potential and corresponding energies becomesincreasingly important for understanding properties of biological macromolecules and theircomplexes. However, this is not an easy task due to the irregular shape of biological entitiesand the presence of water and mobile ions. Results: Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi,enriched with additional features to facilitate DelPhi usage. The suite allows for easydownload of both DelPhi executable files and source code along with a makefile for localinstallations. The users can obtain the DelPhi manual and parameter files required for thecorresponding investigation. Non-experienced researchers can download examples containingall necessary data to carry out DelPhi runs on a set of selected examples illustrating variousDelPhi features and demonstrating DelPhi's accuracy against analytical solutions. Conclusions: DelPhi suite offers not only the DelPhi executable and sources files, examples and parameterfiles, but also provides links to third party developed resources either utilizing DelPhi orproviding plugins for DelPhi. In addition, the users and developers are offered a forum toshare ideas, resolve issues, report bugs and seek help with respect to the DelPhi package. Theresource is available free of charge for academic users from URL:http://compbio.clemson.edu/delphi.php