Estimating statistical distributions using an integral identity

We present an identity for an unbiased estimate of a general statistical distribution. The identity computes the distribution density from dividing a histogram sum over a local window by a correction factor from a mean-force integral, and the mean force can be evaluated as a configuration average. We show that the optimal window size is roughly the inverse of the local mean-force fluctuation. The new identity offers a more robust and precise estimate than a previous one by Adib and Jarzynski [J. Chem. Phys. 122, 014114, (2005)]. It also allows a straightforward generalization to an arbitrary ensemble and a joint distribution of multiple variables. Particularly we derive a mean-force enhanced version of the weighted histogram analysis method (WHAM). The method can be used to improve distributions computed from molecular simulations. We illustrate the use in computing a potential energy distribution, a volume distribution in a constant-pressure ensemble, a radial distribution function and a joint distribution of amino acid backbone dihedral angles.Comment: 45 pages, 7 figures, simplified derivation, a more general mean-force formula, add discussions to the window size, add extensions to WHAM, and 2d distribution

Effect of polydispersity on the relative stability of hard-sphere crystals

By extending the nonequilibrium potential refinement algorithm and lattice switch method to the semigrand ensemble, the semigrand potentials of the fcc and hcp structures of polydisperse hard-sphere crystals are calculated with the bias sampling scheme. The result shows that the fcc structure is more stable than the hcp structure for polydisperse hard-sphere crystals below the terminal polydispersity.Comment: 17 pages, 5 figure

Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces

Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational efficiency based on the assumption that errors are negligible for reasonable cutoffs or compensated for by adjusting other interaction parameters. Arising from a metadynamics study of the wetting transition of water on a solid substrate, we find that the influence of the cutoff is unexpectedly strong and can change the character of the wetting transition from continuous to first order by creating artificial metastable wetting states. Common cutoff corrections such as the use of a force switching function, a shifted potential, or a shifted force do not avoid this. Such a qualitative difference urges caution and suggests that using truncated non-bonded potentials can induce unphysical behavior that cannot be fully accounted for by adjusting other interaction parameters

Scaling Theory and Numerical Simulations of Aerogel Sintering

A simple scaling theory for the sintering of fractal aerogels is presented. The densification at small scales is described by an increase of the lower cut-off length $a$ accompanied by a decrease of the upper cut-off length $\xi$, in order to conserve the total mass of the system. Scaling laws are derived which predict how $a$, $\xi$ and the specific pore surface area $\Sigma$ should depend on the density $\rho$. Following the general ideas of the theory, numerical simulations of sintering are proposed starting from computer simulations of aerogel structure based on a diffusion-limited cluster-cluster aggregation gelling process. The numerical results for $a$, $\xi$ and $\Sigma$ as a function of $\rho$ are discussed according to the initial aerogel density. The scaling theory is only fully recovered in the limit of very low density where the original values of $a$ and $\xi$ are well separated. These numerical results are compared with experiments on partially densified aerogels.Comment: RevTex, 17 pages + 6 postscript figures appended using "uufiles". To appear in J. of Non-Cryst. Solid

Trans-phonon effects in ultrafast nano-devices

We report a novel phenomenon in carbon nanotube (CNT) based devices, the transphonon effects, which resemble the transonic effects in aerodynamics. It is caused by dissipative resonance of nanotube phonons similar to the radial breathing mode, and subsequent drastic surge of the dragging force on the sliding tube, and multiple phonon barriers are encountered as the intertube sliding velocity reaches critical values. It is found that the transphonon effects can be tuned by applying geometric constraints or varying chirality combinations of the nanotubes

Current Algebraic Structures over Manifolds: Poisson Algebras, q-Deformations and Quantization

Poisson algebraic structures on current manifolds (of maps from a finite dimensional Riemannian manifold into a 2-dimensional manifold) are investigated in terms of symplectic geometry. It is shown that there is a one to one correspondence between such current manifolds and Poisson current algebras with three generators. A geometric meaning is given to q-deformations of current algebras. The geometric quantization of current algebras and quantum current algebraic maps is also studied.Comment: 25 pages, Late

On the Construction of Trigonometric Solutions of the Yang-Baxter Equation

We describe the construction of trigonometric R-matrices corresponding to the (multiplicity-free) tensor product of any two irreducible representations of a quantum algebra U_q(\G). Our method is a generalization of the tensor product graph method to the case of two different representations. It yields the decomposition of the R-matrix into projection operators. Many new examples of trigonometric R-matrices (solutions to the spectral parameter dependent Yang-Baxter equation) are constructed using this approach.Comment: latex file, 29 pages, Universitaet Bielefeld and University of Queensland preprint, BI-TP-94/13, UQMATH-94-02 (minor correction: in eq. (4.63) the number 32 should be replaced by 36 and in eq. (4.64) -16 becomes -18 and -10 becomes -8.

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity

Engineering polymer informatics: Towards the computer-aided design of polymers

The computer-aided design of polymers is one of the holy grails of modern chemical informatics and of significant interest for a number of communities in polymer science. The paper outlines a vision for the in silico design of polymers and presents an information model for polymers based on modern semantic web technologies, thus laying the foundations for achieving the vision

Predictive factors of virological success to salvage regimens containing protease inhibitors in HIV-1 infected children

<p>Abstract</p> <p>Background</p> <p>The impact of HIV drug resistance mutations in salvage therapy has been widely investigated in adults. By contrast, data available of predictive value of resistance mutations in pediatric population is scarce.</p> <p>Methods</p> <p>A multicenter, retrospective, observational study was conducted in children who received rescue salvage antiretroviral therapy after virologic failure. CD4 counts and viral load were determined at baseline and 6 months after rescue intervention. Genotypic HIV-1 resistance test and virtual phenotype were assessed at baseline.</p> <p>Results</p> <p>A total of 33 children met the inclusion criteria and were included in the analysis. The median viral load (VL) and median percentage of CD4+ at baseline was 4.0 HIV-RNA log copies/ml and 23.0% respectively. The median duration that children were taking the new rescue regimen was 24.3 weeks (23.8–30.6). Overall, 47% of the 33 children achieved virological response at 24 weeks. When we compared the group of children who achieved virological response with those who did not, we found out that mean number of PI related mutations among the group of responders was 3.8 <it>vs</it>. 5.4 (p = 0.115). Moreover, the mean number of susceptible drugs according to virtual phenotype clinical cut-off for maximal virologic response was 1.7 <it>vs</it>. 0.8 and mean number of susceptible drugs according to virtual phenotype cut-off for minimal virlologic response was 2.7 <it>vs</it>. 1.3 (p < 0.01 in all cases). Eighteen children were rescued with a regimen containing a boosted-PI and virological response was significantly higher in those subjects compared with the others (61.1% <it>vs</it>. 28.6%, p < 0.01).</p> <p>Conclusion</p> <p>Salvage treatment containing ritonavir boosted-PIs in children with virological failure was very efficient. The use of new tools as virtual phenotype could help to improve virologic success in pediatric population.</p