Heterogeneous Diffusion and Nonlinear Advection in a One-Dimensional Fisher-KPP Problem.

The goal of this study is to provide an analysis of a Fisher-KPP non-linear reaction problem with a higher-order diffusion and a non-linear advection. We study the existence and uniqueness of solutions together with asymptotic solutions and positivity conditions. We show the existence of instabilities based on a shooting method approach.

Structural determination of Streptococcus pneumoniae repeat units in serotype 41A and 41F capsular polysaccharides to probe gene functions in the corresponding capsular biosynthetic loci.

We report the repeating unit structures of the native capsular polysaccharides of Streptococcus pneumoniae serotypes 41A and 41F. Structural determinations yielded six carbohydrate units in the doubly branched repeating unit to give the following structure for serotype 41A: The structure determinations were motivated (1) by an ambition to help close the remaining gaps in S. pneumoniae capsular polysaccharide structures, and (2) by the attempt to derive functional annotations of carbohydrate active enzymes in the biosynthesis of bacterial polysaccharides from the determined structures.

MARTINI coarse-grained model for crystalline cellulose microfibers.

Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale and configurational complexity. We have derived a set of MARTINI coarse-grained force field parameters for the simulation of crystalline cellulose fibers.

Determination of native capsular polysaccharide structures of Streptococcus pneumoniae serotypes 39, 42, and 47F and comparison to genetically or serologically related strains.

The diversity of capsular polysaccharides of the bacterial pathogen Streptococcus pneumoniae leads to at least 91 different serotypes. While the genetic loci for capsular biosynthesis have been characterized for all serotypes, the determination of resultant polysaccharide structures remains incomplete. Here, we report the chemical structures of the capsular polysaccharides of serotypes 39, 42, and 47F from the genetic cluster 4, and discuss the structures in the context of structures from serologically and genetically related serotypes.

Structural elucidation of the capsular polysaccharide from Streptococcus pneumoniae serotype 47A by NMR spectroscopy.

The structure of the serotype 47A (Danish nomenclature system) capsular polysaccharide from Streptococcus pneumoniae was elucidated by NMR spectroscopy. The following structure of the repeating heptasaccharide was deduced: [structure: see text]. The serotype 47A capsular polysaccharide is one of 91 structurally and serologically distinct capsular polysaccharides that have been recognized in S.

A coarse-grained model for synergistic action of multiple enzymes on cellulose.

Background: Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units.

Coarse-grained model for the interconversion between native and liquid ammonia-treated crystalline cellulose.

We present the results of Langevin dynamics simulations on a coarse-grained model for a structural transition in crystalline cellulose pertinent to the cellulose degradation problem. We analyze two different cellulose crystalline forms: cellulose Iβ (the natural form of cellulose) and cellulose III(I) (obtained after cellulose Iβ is treated with anhydrous liquid ammonia). Cellulose III(I) has been the focus of wide interest in the field of cellulosic biofuels, as it can be efficiently hydrolyzed to readily fermentable glucose (its enzymatic degradation rates are up to 5-fold higher than those of cellulose Iβ).

Quantum chemical study of carbohydrate-phospholipid interactions.

Carbohydrates on host membranes are fundamental to many important biological processes. Here, we seek a basic understanding of the nature of the interactions between carbohydrates and phospholipids to dissect their roles in molecular recognition. A hybrid quantum mechanics/quantum mechanics (QM/QM) scheme with two different levels of treatment was used to explore the conformations and energetics of carbohydrate-phospholipid complexes.

In silico studies of crystalline cellulose and its degradation by enzymes.

In this report, the current state of computational studies on crystalline cellulose is reviewed. The discussion is focused on fully atomistic molecular-dynamics simulations as well as on other computational approaches which are relevant in the context of enzymatic degradation of cellulose. Finally, possible directions and necessary improvements for future computational studies in this challenging research field are summarized.

Disjoining pressure for nonuniform thin films.

The effect of the attractive forces originating from van der Waals interactions on the dynamics of thin films ( View Article and Find Full Text PDF

Coarse-grained rigid blob model for soft matter simulations.

We have developed a coarse-grained multiscale molecular simulation method for soft matter systems that directly incorporates stereochemical information. We divide the material into disjoint groups of atoms or particles that move as separate rigid bodies; we call these groups "rigid blobs," hence the name coarse-grained rigid blob model. The method is enabled by the construction of transferable interblob potentials that approximate the net intermolecular interactions, as obtained from ab initio electronic structure calculations, other all-atom empirical potentials, experimental data, or any combination of the above.

Capacitance-derived dielectric constants demonstrate differential preinitiation complexes in TBP-independent and TBP-dependent transcription.

The electronic properties of proteins and DNA may change dramatically upon complex formation, yet there are not many experimental methods which can be used to measure these properties. It has been previously shown that measuring the capacitance of a solution containing interacting DNA and protein species can yield information about changing dipole moments. The measured dielectric constant relates directly to the dipole moment of the complexes in solution.

An alternative multipolar expansion for intermolecular potential functions.

We have derived a new multipolar expansion for intermolecular potential-energy functions with applications in molecular physics, theoretical chemistry, and mathematical physics. The new formulation employs a separation of radial and angular terms with a simple index structure that leads to computational efficiency and ease of physical interpretation. For the case of the Coulomb interaction, we compare the present formulation with two conventional multipole expansions: the Cartesian tensor and the irreducible spherical tensor expansions.

Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model.

Aggregation of Fc epsilon RI on mast cells and basophils leads to autophosphorylation and increased activity of the cytosolic protein tyrosine kinase Syk. We investigated the roles of the Src kinase Lyn, the immunoreceptor tyrosine-based activation motifs (ITAMs) on the beta and gamma subunits of Fc epsilon RI, and Syk itself in the activation of Syk. Our approach was to build a detailed mathematical model of reactions involving Fc epsilon RI, Lyn, Syk, and a bivalent ligand that aggregates Fc(epsilon)RI.

Kinetic proofreading in receptor-mediated transduction of cellular signals: receptor aggregation, partially activated receptors, and cytosolic messengers.

Signaling by the T cell receptor (TCR), and the related immunoreceptor Fc epsilon RI, is sensitive to ligand-receptor binding kinetics. Differences in the rate at which a ligand dissociates from a receptor cause disproportionate differences in signaling events and cellular responses to ligand-receptor engagement. Analysis of a simple mathematical model, developed by McKeithan (1995, Proc.

Modeling the early signaling events mediated by FcepsilonRI.

We present a detailed mathematical model of the phosphorylation and dephosphorylation events that occur upon ligand-induced receptor aggregation, for a transfectant expressing FcepsilonRI, Lyn, Syk and endogenous phosphatases that dephosphorylate exposed phosphotyrosines on FcepsilonRI and Syk. Through model simulations we show how changing the ligand concentration, and consequently the concentration of receptor aggregates, can change the nature of a cellular response as well as its amplitude. We illustrate the value of the model in analyzing experimental data by using it to show that the intrinsic rate of dephosphorylation of the FcepsilonRI gamma immunoreceptor tyrosine-based activation motif (ITAM) in rat basophilic leukemia (RBL) cells is much faster than the observed rate, provided that all of the cytosolic Syk is available to receptors.