Dark times: iminothioindoxyl--nucleoside fluorescence quenchers with defined location and minimal perturbation in DNA.

Fluorescence quenchers for application in DNA - like the BHQ family - tend to be large molecules which need to be attached, often post-synthetically, long linkers. In this study, we present two new iminothioindoxyl--nucleosidic quenchers which are very compact, feature a native backbone and can be introduced into DNA regular solid-phase synthesis. Especially with d as juxtaposed nucleobase, they have a defined location and orientation in a DNA duplex with minimal perturbation of the structure and hence interaction capabilities.

Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations.

Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, , activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried , , 2017, , 359].

First-Principles Quantum and Quantum-Classical Simulations of Exciton Diffusion in Semiconducting Polymer Chains at Finite Temperature.

We report on first-principles quantum-dynamical and quantum-classical simulations of photoinduced exciton dynamics in oligothiophene chain segments, representative of intrachain exciton migration in the poly(3-hexylthiophene) (P3HT) polymer. Following up on our recent study (Binder R.; Burghardt, I.

The symmetrical quasi-classical approach to electronically nonadiabatic dynamics applied to ultrafast exciton migration processes in semiconducting polymers.

In the last several years, a symmetrical quasi-classical (SQC) windowing model applied to the classical Meyer-Miller (MM) vibronic Hamiltonian has been shown to be a simple, efficient, general, and quite-accurate method for treating electronically nonadiabatic processes at the totally classical level. Here, the SQC/MM methodology is applied to ultrafast exciton dynamics in a Frenkel/site-exciton model of oligothiophene (OT) as a model of organic semiconductor polymers. In order to keep the electronic representation as compact and efficient as possible, the adiabatic version of the MM Hamiltonian was employed, with dynamical calculations carried out in the recently developed "kinematic momentum" representation, from which site/monomer-specific (diabatic) excitation probabilities were extracted using a new procedure developed in this work.

Multidimensional Langevin Modeling of Nonoverdamped Dynamics.

Based on a given time series, data-driven Langevin modeling aims to construct a low-dimensional dynamical model of the underlying system. When dealing with physical data as provided by, e.g.

Multidimensional Langevin modeling of biomolecular dynamics.

A systematic computational approach to describe the conformational dynamics of biomolecules in reduced dimensionality is presented. The method is based on (i) the decomposition of a high-dimensional molecular dynamics trajectory into a few "system" and (many) "bath" degrees of freedom and (ii) a Langevin simulation of the resulting model. Employing principal component analysis, the dimension of the system is chosen such that it contains all slow large-amplitude motions of the molecule, while the bath coordinates only account for its high-frequency fluctuations.

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis.

A systematic approach to construct a low-dimensional free energy landscape from a classical molecular dynamics (MD) simulation is presented. The approach is based on the recently proposed dihedral angle principal component analysis (dPCA), which avoids artifacts due to the mixing of internal and overall motions in Cartesian coordinates and circumvents problems associated with the circularity of angular variables. Requiring that the energy landscape reproduces the correct number, energy, and location of the system's metastable states and barriers, the dimensionality of the free energy landscape (i.

Dihedral angle principal component analysis of molecular dynamics simulations.

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements.

How complex is the dynamics of Peptide folding?

Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with system size, a Lyapunov analysis shows that the effective dimension of the dynamic system is rather small and even decreases with chain length. The observed reduction of phase space is a nonlinear cooperative effect that is caused by intramolecular hydrogen bonds that stabilize the secondary structure of the peptides.

Practical implementation of nonlinear time series methods: The TISEAN package.

We describe the implementation of methods of nonlinear time series analysis which are based on the paradigm of deterministic chaos. A variety of algorithms for data representation, prediction, noise reduction, dimension and Lyapunov estimation, and nonlinearity testing are discussed with particular emphasis on issues of implementation and choice of parameters. Computer programs that implement the resulting strategies are publicly available as the TISEAN software package.

Dynamical properties of a ferroelectric capacitor observed through nonlinear time series analysis.

By data analysis the ordinary differential equation for the description of an experimental electric resonance circuit with nonlinear capacitor is derived. Triglycine sulfate (TGS) was used as nonlinear dielectric material. This is the most thoroughly investigated ferroelectric with a second order phase transition.

Improved false nearest neighbor method to detect determinism in time series data.

The false nearest neighbor method introduced by Kennel et al. [Phys. Rev.

Estimating the Lyapunov spectrum of time delay feedback systems from scalar time series.

On the basis of a recently developed method for modeling time delay systems, we propose a procedure to estimate the spectrum of Lyapunov exponents from a scalar time series. It turns out that the spectrum is approximated very well and allows for good estimates of the Lyapunov dimension even if the sampling rate of the time series is so low that the infinite dimensional tangent space is spanned quite sparsely.

Optimizing of recurrence plots for noise reduction.

We propose a way to automatically detect the best neighborhood size for a local projective noise reduction filter, where a typical problem is the proper identification of the noise level. Here we make use of concepts from the recurrence quantification analysis in order to adaptively tune the filter along the incoming time series. We define an index, to be computed via recurrence plots, whose minimum gives a clear indication of the best size of the neighborhood in the embedding space.

Analysis of vocal disorders in a feature space.

This paper provides a way to classify vocal disorders for clinical applications. This goal is achieved by means of geometric signal separation in a feature space. Typical quantities from chaos theory (like entropy, correlation dimension and first lyapunov exponent) and some conventional ones (like autocorrelation and spectral factor) are analysed and evaluated, in order to provide entries for the feature vectors.

Convective lyapunov exponents and propagation of correlations.

We conjecture that in one-dimensional spatially extended systems the propagation velocity of correlations coincides with a zero of the convective Lyapunov spectrum. This conjecture is successfully tested in three different contexts: (i) a Hamiltonian system (a Fermi-Pasta-Ulam chain of oscillators); (ii) a general model for spatiotemporal chaos (the complex Ginzburg-Landau equation); (iii) experimental data taken from a CO2 laser with delayed feedback. In the last case, the convective Lyapunov exponent is determined directly from the experimental data.

Denoising human speech signals using chaoslike features.

A local projective noise reduction scheme, originally developed for low-dimensional stationary deterministic chaotic signals, is successfully applied to human speech. This is possible by exploiting properties of the speech signal which resemble structure exhibited by deterministic dynamical systems. In high-dimensional embedding spaces, the strong inherent nonstationarity is resolved as a sequence of many different dynamical regimes of moderate complexity.

Local estimates for entropy densities in coupled map lattices.

We present a method to derive an upper bound for the entropy density of coupled map lattices with local interactions from local observations. To do this, we use an embedding technique that is a combination of time delay and spatial embedding. This embedding allows us to identify the local character of the equations of motion.

Coping with nonstationarity by overembedding.

We discuss how nonstationarity in observed time series data due to pronounced fluctuations of system parameters can be resolved by making use of embedding techniques for scalar data. If a D-dimensional deterministic system is driven by P slowly time dependent parameters, a (D+P)-dimensional manifold has to be reconstructed from the scalar time series, which is done by an m>2(D+P)-dimensional time delay embedding. We show that in this space essential aspects of determinism are restored.

The short DNA sequences in the cytoplasm of Ehrlich ascites tumor cells are tightly associated with proteins.

Mouse Ehrlich tumor cells harbor extrachromosomal DNA elements in a non-mitochondrial fraction of the cytoplasm (Abken et al., Proc. Natl.