Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains

Previously, we described a coarse-graining method for creating local density-dependent implicit solvent (DDIS) potentials that reproduce the radial distribution function (RDF) and solute excess chemical potential across a range of particle concentrations [ E. C. Allen and G. C. Rutledge, J. Chem. Phys. 128, 154115 (2008) ]. In this work, we test the transferability of these potentials, derived from simulations of monomeric solute in monomeric solvent, to mixtures of solutes and to solute chains in the same monomeric solvent. For this purpose, “transferability” refers to the predictive capability of the potentials without additional optimization. We find that RDF transferability to mixtures is very good, while RDF errors in systems of chains increase linearly with chain length. Excess chemical potential transferability is good for mixtures at low solute concentration, chains, and chains of mixed composition; at higher solute concentrations in mixtures, chemical potential transferability fails due to the nature of the DDIS potentials, in which particle insertion directly affects the interaction potential. With these results, we demonstrate that DDIS potentials derived for pure solutes can be used effectively in the study of many important systems including those involving mixtures, chains, and chains of mixed composition in monomeric solvent.United States. Dept. of Energy (Computational Sciences Graduate Fellowship

What information theory can tell us about quantum reality

An investigation of Einstein's ``physical'' reality and the concept of quantum reality in terms of information theory suggests a solution to quantum paradoxes such as the Einstein-Podolsky-Rosen (EPR) and the Schroedinger-cat paradoxes. Quantum reality, the picture based on unitarily evolving wavefunctions, is complete, but appears incomplete from the observer's point of view for fundamental reasons arising from the quantum information theory of measurement. Physical reality, the picture based on classically accessible observables is, in the worst case of EPR experiments, unrelated to the quantum reality it purports to reflect. Thus, quantum information theory implies that only correlations, not the correlata, are physically accessible: the mantra of the Ithaca interpretation of quantum mechanics.Comment: LaTeX with llncs.cls, 11 pages, 6 postscript figures, Proc. of 1st NASA Workshop on Quantum Computation and Quantum Communication (QCQC 98

Coarse-graining strategies in polymer solutions

We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to reproduce some coarse-grained features of the zero-density isolated-chain structure. By tuning the level of coarse graining, i.e. the number of monomers to be mapped onto a single blob, the model should be adequate to explore the semidilute regime above the collapse transition, since in this case the monomer density is very small if chains are long enough. The implementation of these ideas has been previously based on a transferability hypothesis, which was not completely tested against full-monomer results (Pierleoni et al., J. Chem. Phys, 127, 171102 (2007)). We study different models proposed in the past and we compare their predictions to full-monomer results for the chain structure and the thermodynamics in the range of polymer volume fractions \Phi between 0 and 8. We find that the transferability assumption has a limited predictive power if a thermodynamically consistent model is required. We introduce a new tetramer model parametrized in such a way to reproduce not only zero-density intramolecular and intermolecular two-body probabilities, but also some intramolecular three-body and four-body distributions. We find that such a model correctly predicts three-chain effects, the structure and the thermodynamics up to \Phi ~ 2, a range considerably larger than that obtained with previous simpler models using zero-density potentials. Our results show the correctness of the ideas behind the multiblob approach but also that more work is needed to understand how to develop models with more effective monomers which would allow us to explore the semidilute regime at larger chain volume fractions.Comment: 33 pages, 19 figures, submitted to Soft Matte

Novel highly potent CD4bs bNAb with restricted pathway to HIV-1 escape

Purpose: Broadly HIV-1 neutralizing antibodies (bNAbs) can suppress viremia in humans and represent a novel approach for effective immunotherapy. However, bNAb monotherapy selects for antibody-resistant viral variants. Thus, we focused on the identification of new antibody combinations and/or novel bNAbs that restrict pathways of HIV-1 escape. Methods: We screened HIV-1 positive patients for their neutralizing capacities. Following, we performed single cell sorting and PCR of HIV-1 Env-reactive mature B cells of identified elite neutralizers. Found antibodies were tested for neutralization and binding capacities in vitro. Further, their antiviral activity was tested in an HIV-1 infected humanized mouse model. Results: Here we report the isolation of antibody 1–18, a VH1–46-encoded CD4 binding site (CD4bs) bNAb identified in an individual ranking among the top 1% neutralizers of 2,274 HIV-1-infected subjects. Tested on a 119-virus panel, 1–18 showed to be exceptionally broad and potent with a coverage of 97% and a mean IC50 of 0.048 lg/mL, exceeding the activity of most potent CD4bs bNAbs described to-date. A 2.4 Å cryo-EM structure of 1–18 bound to a native-like Env trimer revealed that it interacts with HIV-1 env similar to other CD4bs bNAbs, but includes additional contacts to the V3 loop of the adjacent protomer. Notably, in vitro, 1–18 maintained activity against viruses carrying mutations associated with escape from VRC01-class bNAbs. Further, its HIV-1 env wide escape profile differed critically from other CD4bs bNAbs. In humanized mice, monotherapy with 1–18 was sufficient to prevent the development of viral escape variants that rapidly emerged during treatment with other CD4bs bNAbs. Finally, 1–18 overcame classical HIV-1 mutations that are driven by VRC01-like bNAbs in vivo. Conclusion: 1–18 is a highly potent and broad bNAb that restricts escape and overcomes frequent CD4bs escape pathways, providing new options for bNAb combinations to prevent and treat HIV-1 infection