QC-DMRG study of the ionic--neutral curve crossing of LiF

We have studied the ionic--neutral curve crossing between the two lowest ^1 Sigma^+ states of LiF in order to demonstrate the efficiency of the quantum chemistry version of the density matrix renormalization group method (QC-DMRG). We show that QC-DMRG is capable to calculate the ground and several low-lying excited state energies within the error margin set up in advance of the calculation, while with standard quantum chemical methods it is difficult to obtain a good approximation to Full CI property values at the point of the avoided crossing. We have calculated the dipole moment as a function of bond length, which in fact provides a smooth and continuous curve even close to the avoided crossing, in contrast to other standard numerical treatments.Comment: 10 pages, 6 figure

Spin-resolved electron-impact ionization of lithium

Electron-impact ionization of lithium is studied using the convergent close-coupling (CCC) method at 25.4 and 54.4 eV. Particular attention is paid to the spin-dependence of the ionization cross sections. Convergence is found to be more rapid for the spin asymmetries, which are in good agreement with experiment, than for the underlying cross sections. Comparison with the recent measured and DS3C-calculated data of Streun et al (1999) is most intriguing. Excellent agreement is found with the measured and calculated spin asymmetries, yet the discrepancy between the CCC and DS3C cross sections is very large

Analysis of the Ub to Ub-CR Transition in Ubiquitin.

A new conformation has recently been reported for ubiquitin (Ub). This invisible conformation (Ub-CR), where the C-terminal tail is retracted, has a key functional role in phosphorylation of the Ser65 residue, a trigger for PINK1 and Parkin dependent mitophagy. Here we calculate the transition mechanism and associated rates for the Ub to Ub-CR pathway in the wild-type protein and a selection of mutants. We predict a cooperative one-step process with a transition state that resembles the Ub configuration, characterized by a loss of all interactions of the C-terminal tail with surrounding residues, and an open ubiquitin scaffold. The calculated observables agree well with reported values, and we make a range of predictions to guide future experiments. In particular, the effect of mutations on the pathway and the corresponding structural ensembles should have observable consequences. This feedback between theory and experiment promises new insight into key cellular processes.EPSR

Energy Landscapes for the Aggregation of Aβ17-42.

The aggregation of the Aβ peptide (Aβ1-42) to form fibrils is a key feature of Alzheimer's disease. The mechanism is thought to be a nucleation stage followed by an elongation process. The elongation stage involves the consecutive addition of monomers to one end of the growing fibril. The aggregation process proceeds in a stop-and-go fashion and may involve off-pathway aggregates, complicating experimental and computational studies. Here we present exploration of a well-defined region in the free and potential energy landscapes for the Aβ17-42 pentamer. We find that the ideal aggregation process agrees with the previously reported dock-lock mechanism. We also analyze a large number of additional stable structures located on the multifunnel energy landscape, which constitute kinetic traps. The key contributors to the formation of such traps are misaligned strong interactions, for example the stacking of F19 and F20, as well as entropic contributions. Our results suggest that folding templates for aggregation are a necessity and that aggregation studies could employ such species to obtain a more detailed description of the process

Mutational Basin-Hopping: Combined Structure and Sequence Optimization for Biomolecules.

The study of energy landscapes has led to a good understanding of how and why proteins and nucleic acids adopt their native structure. Through evolution, sequences have adapted until they exhibit a strongly funneled energy landscape, stabilizing the native fold. Design of artificial biomolecules faces the challenge of creating similar stable, minimally frustrated, and functional sequences. Here we present a biminimization approach, mutational basin-hopping, in which we simultaneously use global optimization to optimize the energy and a target function describing a desired property of the system. This optimization of structure and sequence is a generalized basin-hopping method and produces an efficient design process, which can target properties such as binding affinity or solubility

Object oriented databases in software development for structural analysis

A technique for using object-oriented technologies to write structural analysis software has been developed. The structural design information of an individual building is stored in an object-oriented database. A global database provides general design values as material data and safety factors. A class library for load elements has been evolved to model the transfer of loads in a building. This class library is the basis for the development of further classes for other structural elements such as beams, columns or slabs. A software has been developed to monitor the forces transferred from one structural member to another in a building for load cases and combinations according to Eurocode 1. The results of the analysis are stored in the projects database from which a structural design report may be generated. The software was developed under Microsoft Visual C++. The Microsoft Foundation Class Library (MFC) was used to program the Graphical User Interface (GUI). Object Linking and Embedding (OLE) technology is useful to include any type of OLE server objects for example texts written with a word processor or CAD drawings in the structural design report. The Object-Oriented Database Management System (OODBMS) ObjectStore provides services to store the large amount of objects

Post-training load-related changes of auditory working memory: An EEG study

Working memory (WM) refers to the temporary retention and manipulation of information, and its capacity is highly susceptible to training. Yet, the neural mechanisms that allow for increased performance under demanding conditions are not fully understood. We expected that post-training efficiency in WM performance modulates neural processing during high load tasks. We tested this hypothesis, using electroencephalography (EEG) (N = 39), by comparing source space spectral power of healthy adults performing low and high load auditory WM tasks. Prior to the assessment, participants either underwent a modality-specific auditory WM training, or a modality-irrelevant tactile WM training, or were not trained (active control). After a modality-specific training participants showed higher behavioral performance, compared to the control. EEG data analysis revealed general effects of WM load, across all training groups, in the theta-, alpha-, and beta-frequency bands. With increased load theta-band power increased over frontal, and decreased over parietal areas. Centro-parietal alpha-band power and central beta-band power decreased with load. Interestingly, in the high load condition a tendency toward reduced beta-band power in the right medial temporal lobe was observed in the modality-specific WM training group compared to the modality-irrelevant and active control groups. Our finding that WM processing during the high load condition changed after modality-specific WM training, showing reduced beta-band activity in voice-selective regions, possibly indicates a more efficient maintenance of task-relevant stimuli. The general load effects suggest that WM performance at high load demands involves complementary mechanisms, combining a strengthening of task-relevant and a suppression of task-irrelevant processing

Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.

Artificial analogues of the natural nucleic acids have attracted interest as a diverse class of information storage molecules capable of self-replication. In this study, we use the computational potential energy landscape framework to investigate the structural and dynamical properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA), which are derived from their respective RNA and DNA analogues by inversion of a single chiral center in the sugar moiety of the nucleotides. For an octameric XyNA sequence and the analogue dXyNA, we observe facile conformational transitions between a left-handed helix, which is the free energy global minimum, and a ladder-type structure with approximately zero helicity. The competing ensembles are better separated in the dXyNA, making it a more suitable candidate for a molecular switch, whereas the XyNA exhibits additional flexibility. Both energy landscapes exhibit greater frustration than we observe in RNA or DNA, in agreement with the higher degree of optimization expected from the principle of minimal frustration in evolved biomolecules