Variational Perturbation Theory for Fokker-Planck Equation with Nonlinear Drift

We develop a recursive method for perturbative solutions of the Fokker-Planck equation with nonlinear drift. The series expansion of the time-dependent probability density in terms of powers of the coupling constant is obtained by solving a set of first-order linear ordinary differential equations. Resumming the series in the spirit of variational perturbation theory we are able to determine the probability density for all values of the coupling constant. Comparison with numerical results shows exponential convergence with increasing order.Comment: Author Information under http://www.theo-phys.uni-essen.de/tp/ags/pelster_dir

amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R.

Можливості ефективної організації та стимулювання бажаних трансформацій

У статті розглядається поняття інформаційного впливу як багаторівневого феномена. Вводиться розмежування між інформаційними впливами під час взаємодії різних соціальних систем і змальовано ефект інформаційного впливу на соціально-економічний розвиток суспільства. У статті автор продовжує аналіз власної концепції розвитку соціальних технологій постмодерного м’якого управління з точки зору стану національної безпеки. Він розробляє модель постмодерного інформаційного впливу – стимулювання бажаних змін.The article examines the notion of information influence as a multilevel phenomenon. The division is applied between information influence of different social systems interaction and the impact of information influence upon society’s social and economic development is shown. In the article the author continues analysis of his conception of postmodern soft management social technologies development from the point of view of national security situation. He elaborates the model of postmodern information influence – desirable changes stimulation

Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures

Here, using an integrative experimental and computational approach, Imle et al. show how cell motility and density affect HIV cell-associated transmission in a three-dimensional tissue-like culture system of CD4+ T cells and collagen, and how different collagen matrices restrict infection by cell-free virions

amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R

Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.Comment: 15 pages, 17 figures, submitted to Eur. J. Phys.

Computational protein profile similarity screening for quantitative mass spectrometry experiments

Motivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account. Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method

New Optimization Methods for Converging Perturbative Series with a Field Cutoff

We take advantage of the fact that in lambda phi ^4 problems a large field cutoff phi_max makes perturbative series converge toward values exponentially close to the exact values, to make optimal choices of phi_max. For perturbative series terminated at even order, it is in principle possible to adjust phi_max in order to obtain the exact result. For perturbative series terminated at odd order, the error can only be minimized. It is however possible to introduce a mass shift in order to obtain the exact result. We discuss weak and strong coupling methods to determine the unknown parameters. The numerical calculations in this article have been performed with a simple integral with one variable. We give arguments indicating that the qualitative features observed should extend to quantum mechanics and quantum field theory. We found that optimization at even order is more efficient that at odd order. We compare our methods with the linear delta-expansion (LDE) (combined with the principle of minimal sensitivity) which provides an upper envelope of for the accuracy curves of various Pade and Pade-Borel approximants. Our optimization method performs better than the LDE at strong and intermediate coupling, but not at weak coupling where it appears less robust and subject to further improvements. We also show that it is possible to fix the arbitrary parameter appearing in the LDE using the strong coupling expansion, in order to get accuracies comparable to ours.Comment: 10 pages, 16 figures, uses revtex; minor typos corrected, refs. adde

Perturbation Theory for Path Integrals of Stiff Polymers

The wormlike chain model of stiff polymers is a nonlinear $\sigma$-model in one spacetime dimension in which the ends are fluctuating freely. This causes important differences with respect to the presently available theory which exists only for periodic and Dirichlet boundary conditions. We modify this theory appropriately and show how to perform a systematic large-stiffness expansions for all physically interesting quantities in powers of $L/\xi$, where $L$ is the length and $\xi$ the persistence length of the polymer. This requires special procedures for regularizing highly divergent Feynman integrals which we have developed in previous work. We show that by adding to the unperturbed action a correction term ${\cal A}^{\rm corr}$, we can calculate all Feynman diagrams with Green functions satisfying Neumann boundary conditions. Our expansions yield, order by order, properly normalized end-to-end distribution function in arbitrary dimensions $d$, its even and odd moments, and the two-point correlation function

Performance of ab initio and density functional methods for conformational equilibria of CnH2n+2 alkane isomers (n=2-8)

Conformational energies of n-butane, n-pentane, and n-hexane have been calculated at the CCSD(T) level and at or near the basis set limit. Post-CCSD(T) contribution were considered and found to be unimportant. The data thus obtained were used to assess the performance of a variety of density functional methods. Double-hybrid functionals like B2GP-PLYP and B2K-PLYP, especially with a small Grimme-type empirical dispersion correction, are capable of rendering conformational energies of CCSD(T) quality. These were then used as a `secondary standard' for a larger sample of alkanes, including isopentane and the branched hexanes as well as key isomers of heptane and octane. Popular DFT functionals like B3LYP, B3PW91, BLYP, PBE, and PBE0 tend to overestimate conformer energies without dispersion correction, while the M06 family severely underestimates GG interaction energies. Grimme-type dispersion corrections for these overcorrect and lead to qualitatively wrong conformer orderings. All of these functionals also exhibit deficiencies in the conformer geometries, particularly the backbone torsion angles. The PW6B95 and, to a lesser extent, BMK functionals are relatively free of these deficiencies. Performance of these methods is further investigated to derive conformer ensemble corrections to the enthalpy function, $H_{298}-H_0$, and the Gibbs energy function, ${\rm gef}(T)\equiv - [G(T)-H_0]/T$, of these alkanes. While $H_{298}-H_0$ is only moderately sensitive to the level of theory, ${\rm gef}(T)$ exhibits more pronounced sensitivity. Once again, double hybrids acquit themselves very well.Comment: J. Phys. Chem. A, revised [Walter Thiel festschrift