Soft core thermodynamics from self-consistent hard core fluids

In an effort to generalize the self-consistent Ornstein-Zernike approximation (SCOZA) -- an accurate liquid-state theory that has been restricted so far to hard-core systems -- to arbitrary soft-core systems we study a combination of SCOZA with a recently developed perturbation theory. The latter was constructed by Ben-Amotz and Stell [J. Phys. Chem. B 108,6877-6882 (2004)] as a reformulation of the Week-Chandler-Andersen perturbation theory directly in terms of an arbitrary hard-sphere reference system. We investigate the accuracy of the combined approach for the Lennard-Jones fluid by comparison with simulation data and pure perturbation theory predictions and determine the dependence of the thermodynamic properties and the phase behavior on the choice of the effective hard-core diameter of the reference system.Comment: 38 pages, 10 figure

A proof of Jarzynski's non-equilibrium work theorem for dynamical systems that conserve the canonical distribution

We present a derivation of the Jarzynski identity and the Crooks fluctuation theorem for systems governed by deterministic dynamics that conserves the canonical distribution such as Hamiltonian dynamics, Nose-Hoover dynamics, Nose-Hoover chains and Gaussian isokinetic dynamics. The proof is based on a relation between the heat absorbed by the system during the non-equilibrium process and the Jacobian of the phase flow generated by the dynamics.Comment: 12 page

Liquid-vapor transition of systems with mean field universality class

We have considered a system where the interaction, v(r) = v_IS(r) + xi^2 v_MF(r), is given as a linear combination of two potentials, each of which being characterized with a well-defined critical behavior: for v_IS(r) we have chosen the potential of the restricted primitive model which is known to belong to the Ising 3D (IS) universality class, while for v_MF(r) we have considered a long-range interaction in the Kac-limit, displaying mean field (MF) behavior. We study the performance of two theoretical approaches and of computer simulations in the critical region for this particular system and give a detailed comparison between theories and simulation of the critical region and the location of the critical point. Both, theory and simulation give evidence that the system belongs to the MF universality class for any positive value of xi and that it shows only non-classical behavior for xi=0. While in this limiting case theoretical approaches are known to fail, we find good agreement for the critical properties between the theoretical approaches and the simulations for xi^2 larger than 0.05.Comment: 9 pages, 11 figures, 3 table

A numerical study of a binary Yukawa model in regimes characteristic of globular proteins in solutions

The main goal of this paper is to assess the limits of validity, in the regime of low concentration and strong Coulomb coupling (high molecular charges), for a simple perturbative approximation to the radial distribution functions (RDF), based upon a low-density expansion of the potential of mean force and proposed to describe protein-protein interactions in a recent Small-Angle-Scattering (SAS) experimental study. A highly simplified Yukawa (screened Coulomb) model of monomers and dimers of a charged globular protein ($\beta$-lactoglobulin) in solution is considered. We test the accuracy of the RDF approximation, as a necessary complementary part of the previous experimental investigation, by comparison with the fluid structure predicted by approximate integral equations and exact Monte Carlo (MC) simulations. In the MC calculations, an Ewald construction for Yukawa potentials has been used to take into account the long-range part of the interactions in the weakly screened cases. Our results confirm that the perturbative first-order approximation is valid for this system even at strong Coulomb coupling, provided that the screening is not too weak (i.e., for Debye length smaller than monomer radius). A comparison of the MC results with integral equation calculations shows that both the hypernetted-chain (HNC) and the Percus-Yevick (PY) closures have a satisfactory behavior under these regimes, with the HNC being superior throughout. The relevance of our findings for interpreting SAS results is also discussed.Comment: Physical Review E, in press (2005

N-glycomic Complexity in Anatomical Simplicity: Caenorhabditis elegans as a Non-model Nematode?

Caenorhabditis elegans is a genetically well-studied model nematode or “worm”; however, its N-glycomic complexity is actually baffling and still not completely unraveled. Some features of its N-glycans are, to date, unique and include bisecting galactose and up to five fucose residues associated with the asparagine-linked Man2−3GlcNAc2 core; the substitutions include galactosylation of fucose, fucosylation of galactose and methylation of mannose or fucose residues as well as phosphorylcholine on antennal (non-reducing) N-acetylglucosamine. Only some of these modifications are shared with various other nematodes, while others have yet to be detected in any other species. Thus, C. elegans can be used as a model for some aspects of N-glycan function, but its glycome is far from identical to those of other organisms and is actually far from simple. Possibly the challenges of its native environment, which differ from those of parasitic or necromenic species, led to an anatomically simple worm possessing a complex glycome

The Glycosylation Capacity of Insect Cells

It is generally accepted that insects primarily synthesise oligomannosidic and paucimannosidic N-glycan structures. Indeed, insects’ capability to produce human-like complex type N-glycans has been a matter of controversy for a number of years. The relative or complete lack of these structures was primarily attributed to low (or undetectable) activities of the glycosyltransferases needed to drive the synthesis of hybrid and complex type N-glycans (i.e., b-1,2-N-acetylglucosaminyltransferases I and II, b-1,4-galactosyltransferase, a-2,3- and a-2,6-sialyltransferases). Recent developments, fuelled by availability of genomic sequences and by advances in relevant methodologies, have shed some light on the subject, with a few unexpected twists. The identification of a transmembrane/Golgi hexosaminidase, an enzyme which removes a non-reducing N-acetylglucosamine residue during N-glycan biosynthesis, has demonstrated that the synthesis of complex-type N-glycans is actively and deliberately being prevented in insects. On the other hand, the characterisation of an active a-2,6-sialyltransferase in Drosophila, combined with the occurrence of sialylated N-glycan structures as detected in a detailed analysis of Drosophila embryos, has clearly shown that insects can, and need to, synthesise low levels of these structures. The current understanding of the insect N-glycan biosynthetic pathways taking place in Golgi apparatus and trans-Golgi network are elaborated and discussed

Theoretical description of phase coexistence in model C60

We have investigated the phase diagram of the Girifalco model of C60 fullerene in the framework provided by the MHNC and the SCOZA liquid state theories, and by a Perturbation Theory (PT), for the free energy of the solid phase. We present an extended assessment of such theories as set against a recent Monte Carlo study of the same model [D. Costa et al, J. Chem. Phys. 118:304 (2003)]. We have compared the theoretical predictions with the corresponding simulation results for several thermodynamic properties. Then we have determined the phase diagram of the model, by using either the SCOZA, or the MHNC, or the PT predictions for one of the coexisting phases, and the simulation data for the other phase, in order to separately ascertain the accuracy of each theory. It turns out that the overall appearance of the phase portrait is reproduced fairly well by all theories, with remarkable accuracy as for the melting line and the solid-vapor equilibrium. The MHNC and SCOZA results for the liquid-vapor coexistence, as well as for the corresponding critical points, are quite accurate. All results are discussed in terms of the basic assumptions underlying each theory. We have selected the MHNC for the fluid and the first-order PT for the solid phase, as the most accurate tools to investigate the phase behavior of the model in terms of purely theoretical approaches. The overall results appear as a robust benchmark for further theoretical investigations on higher order C(n>60) fullerenes, as well as on other fullerene-related materials, whose description can be based on a modelization similar to that adopted in this work.Comment: RevTeX4, 15 pages, 7 figures; submitted to Phys. Rev.

Structure of ternary additive hard-sphere fluid mixtures

Monte Carlo simulations on the structural properties of ternary fluid mixtures of additive hard spheres are reported. The results are compared with those obtained from a recent analytical approximation [S. B. Yuste, A. Santos, and M. Lopez de Haro, J. Chem. Phys. 108, 3683 (1998)] to the radial distribution functions of hard-sphere mixtures and with the results derived from the solution of the Ornstein-Zernike integral equation with both the Martynov-Sarkisov and the Percus-Yevick closures. Very good agreement between the results of the first two approaches and simulation is observed, with a noticeable improvement over the Percus-Yevick predictions especially near contact.Comment: 11 pages, including 8 figures; A minor change; accepted for publication in PR

Identification and functional characterization of a highly divergent N-acetylglucosaminyltransferase I (TbGnTI) in <em>Trypanosoma brucei</em>

Trypanosoma brucei expresses a diverse repertoire of N-glycans, ranging from oligomannose and paucimannose structures to exceptionally large complex N-glycans. Despite the presence of the latter, no obvious homologues of known β1–4-galactosyltransferase or β1–2- or β1–6-N-acetylglucosaminyltransferase genes have been found in the parasite genome. However, we previously reported a family of putative UDP-sugar-dependent glycosyltransferases with similarity to the mammalian β1–3-glycosyltransferase family. Here we characterize one of these genes, TbGT11, and show that it encodes a Golgi apparatus resident UDP-GlcNAc:α3-d-mannoside β1–2-N-acetylglucosaminyltransferase I activity (TbGnTI). The bloodstream-form TbGT11 null mutant exhibited significantly modified protein N-glycans but normal growth in vitro and infectivity to rodents. In contrast to multicellular organisms, where the GnTI reaction is essential for biosynthesis of both complex and hybrid N-glycans, T. brucei TbGT11 null mutants expressed atypical “pseudohybrid” glycans, indicating that TbGnTII activity is not dependent on prior TbGnTI action. Using a functional in vitro assay, we showed that TbGnTI transfers UDP-GlcNAc to biantennary Man(3)GlcNAc(2), but not to triantennary Man(5)GlcNAc(2), which is the preferred substrate for metazoan GnTIs. Sequence alignment reveals that the T. brucei enzyme is far removed from the metazoan GnTI family and suggests that the parasite has adapted the β3-glycosyltransferase family to catalyze β1–2 linkages