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

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

Transient State Work Fluctuation Theorem for a Driven Classical System

We derive the nonequilibrium transient state work fluctuation theorem and also the Jarzynski equality for a classical harmonic oscillator linearly coupled to a harmonic heat bath, which is dragged by an external agent. Coupling with the bath makes the dynamics not only dissipative but also non-Markovian in general. Since we do not assume anything about the spectral nature of the harmonic bath the derivation is not only restricted to the Markovian bath rather it is more general, for a non-Markovian bath

Ancestral roles of the Fam20C family of secreted protein kinases revealed in C. elegans.

Fam20C is a secreted protein kinase mutated in Raine syndrome, a human skeletal disorder. In vertebrates, bone and enamel proteins are major Fam20C substrates. However, Fam20 kinases are conserved in invertebrates lacking bone and enamel, suggesting other ancestral functions. We show that FAMK-1, the Caenorhabditis elegans Fam20C orthologue, contributes to fertility, embryogenesis, and development. These functions are not fulfilled when FAMK-1 is retained in the early secretory pathway. During embryogenesis, FAMK-1 maintains intercellular partitions and prevents multinucleation; notably, temperature elevation or lowering cortical stiffness reduces requirement for FAMK-1 in these contexts. FAMK-1 is expressed in multiple adult tissues that undergo repeated mechanical strain, and selective expression in the spermatheca restores fertility. Informatic, biochemical, and functional analysis implicate lectins as FAMK-1 substrates. These findings suggest that FAMK-1 phosphorylation of substrates, including lectins, in the late secretory pathway is important in embryonic and tissue contexts where cells are subjected to mechanical strain

A human embryonic kidney 293T cell line mutated at the Golgi -mannosidase II locus

Disruption of Golgi -mannosidase II activity can result in type II congenital dyserythropoietic anemia and can induce lupus-like autoimmunity in mice. Here, we isolate a mutant human embryonic kidney (HEK) 293T cell line, called Lec36, that displays sensitivity to ricin that lies between the parental HEK 293T cells, whose secreted and membrane-expressed proteins are dominated by complex-type glycosylation, and 293S Lec1 cells, which only produce oligomannose-type N-linked glycans. The stem cell marker, 19A, was transiently expressed in the HEK 293T Lec36 cells, and in parental HEK 293T cells with and without the potent Golgi -mannosidase II inhibitor, swainsonine. Negative-ion nano-electrospray ionization mass spectra of the 19A N-linked glycans from HEK 293T Lec36 and swainsonine-treated HEK 293T cells were qualitatively indistinguishable and, as shown by collision-induced dissociation spectra, dominated by hybrid-type glycosylation. Nucleotide sequencing revealed mutations in each allele of MAN2A1, the gene encoding Golgi -mannosidase II: a point mutation in one allele mapping to the active site and an in-frame deletion of twelve-nucleotides in the other. Expression of wild-type but not the mutant MAN2A1 alleles in Lec36 cells restored processing of the 19A reporter glycoprotein to complex-type glycosylation. The Lec36 cell line will be useful for expressing therapeutic glycoproteins with hybrid-type glycans and provides a sensitive host for detecting mutations in human MAN2A1 causing type II congenital dyserythropoietic anemia

Continuous demixing at liquid-vapor coexistence in a symmetrical binary fluid mixture

We report a Monte Carlo finite-size scaling study of the demixing transition of a symmetrical Lennard-Jones binary fluid mixture. For equal concentration of species, and for a choice of the unlike-to-like interaction ratio delta=0.7, this transition is found to be continuous at liquid-vapor coexistence. The associated critical end point exhibits Ising-like universality. These findings confirm those of earlier smaller scale simulation studies of the same model, but contradict the findings of recent integral equation and hierarchical reference theory investigations.Comment: 7 pages, 6 figure

Insights into the salivary<i>N</i>-glycome of<i>Lutzomyia longipalpis</i>, vector of visceral leishmaniasis

AbstractDuringLeishmaniatransmission sand flies inoculate parasites and saliva into the skin of vertebrates. Saliva has anti-haemostatic and anti-inflammatory activities that evolved to facilitate bloodfeeding, but also modulate the host’s immune responses. Sand fly salivary proteins have been extensively studied, but the nature and biological roles of protein-linked glycans remain overlooked. Here, we characterised the profile ofN-glycans from the salivary glycoproteins ofLutzomyia longipalpis, vector of visceral leishmaniasis in the Americas.In silicopredictions suggest half ofLu. longipalpissalivary proteins may beN-glycosylated. SDS-PAGE coupled to LC-MS analysis of sand fly saliva, before and after enzymatic deglycosylation, revealed several candidate glycoproteins. To determine the diversity ofN-glycan structures in sand fly saliva, enzymatically released sugars were fluorescently tagged and analysed by HPLC, combined with highly sensitive LC-MS/MS, MALDI-TOF-MS, and exoglycosidase treatments. We found that theN-glycan composition ofLu. longipalpissaliva mostly consists of oligomannose sugars, with Man5GlcNAc2being the most abundant, and a few hybrid-type species. Interestingly, some glycans appear modified with a group of 144 Da, whose identity has yet to be confirmed. Our work presents the first detailed structural analysis of sand fly salivary glycans.</jats:p