Unveiling oxygen vacancy impact on lizardite thermo and mechanical properties

Here, we performed a systematic DFT study assisted by the workflow framework SimStack for the mechanical and thermodynamic properties of the clay mineral lizardite in pristine and six different types of O vacancies configurations. In most cases, the defect caused a structural phase transition in the lizardite from the trigonal (pristine) to the triclinic phase. The results show that oxygen vacancies in lizardite significantly reduce the lattice thermal conductivity, accompanied by an elastic moduli reduction and an anisotropy index increase. Through the P-V relation, an increase in compressibility was evidenced for vacancy configurations. Except for the vacancy with the same crystalline structure as pristine lizardite, the sound velocities of the other vacancy configurations produce a decrease in these velocities, and it is essential to highlight high values for the Grüneisen parameter. We emphasize the great relevance of the punctual-defects introduction, such as O vacancies, in lizardite, since this microstructural design is responsible for the decrease of the lattice thermal conductivity in comparison with the pristine system by decreasing the heat transfer ability, turning lizardite into a promising candidate for thermoelectric materials.

How cation nature controls the bandgap and bulk Rashba splitting of halide perovskites

Because of instability issues presented by metal halide perovskites based on methylammonium (MA), its replacement to Cs $$ \mathrm{Cs} $$ has emerged as an alternative to improve the materials' durability. However, the impact of this replacement on electronic properties, especially gap energy and bulk Rashba splitting remains unclear since electrostatic interactions from organic cations can play a crucial role. Through first-principles calculations, we investigated how organic/inorganic cations impact the electronic properties of MAPbI 3 $$ {\mathrm{MAPbI}}_3 $$ and CsPbI 3 $$ {\mathrm{CsPbI}}_3 $$ perovskites. Although at high temperatures the organic cation can assume spherical-like configurations due to its rotation into the cages, our results provide a complete electronic mechanism to show, from a chemical perspective based on ab initio calculations at 0 K $$ 0\ \mathrm{K} $$ , how the MA $$ \mathrm{MA} $$ dipoles suppression can reduce the MAPbI 3 $$ {\mathrm{MAPbI}}_3 $$ gap energy by promoting a degeneracy breaking in the electronic states from the PbI 3 $$ {\mathrm{PbI}}_3 $$ framework, while the dipole moment reinforcement is crucial to align theory ↔ $$ \leftrightarrow $$ experiment, increasing the bulk Rashba splitting through higher Pb $$ \mathrm{Pb} $$ off-centering motifs. The lack of permanent dipole moment in Cs $$ \mathrm{Cs} $$ results in CsPbI 3 $$ {\mathrm{CsPbI}}_3 $$ polymorphs with a pronounced Pb $$ \mathrm{Pb} $$ on-centering-like feature, which causes suppression in their respective bulk Rashba effect.

Determination of specific and non-specific protein-protein interactions for beta-lactoglobulin by analytical ultracentrifugation and membrane osmometry experiments

Protein-protein interactions are essential for the understanding of biological processes. Specific protein aggregation is an important aspect for many biological systems. In particular, electrostatic interactions play the key role for protein-protein interactions, as many amino acids have pH-dependent charge states. Moreover, protein dissociation is directly related to the solution pH, ionic strength, temperature and protein concentration. The subtle interplay between different specific and non-specific interactions is demonstrated for beta-lactoglobulin (BLG) with a focus on low salt concentrations, thus mimicking technically relevant processing conditions. BLG is a well-characterized model system, proven to attain its monomer-dimer equilibrium strongly dependent upon the pH of the solution. In this manuscript, we present a unique combination of analytical ultracentrifugation and membrane osmometry experiments, which quantifies specific and non-specific interactions, i.e. in terms of the dimer dissociation constants and the second osmotic virial coefficient, at pH 3 and 7 and sodium chloride concentrations of 10 mM and 100 mM. This provides direct insight to protein-protein interactions for a system with a concentration-dependent monomer-dimer equilibrium. Moreover, using a coarse-grained extended DLVO model in combination with molecular dynamics simulations, we quantify non-specific monomer-monomer, monomer-dimer and dimer-dimer interactions as well as the binding free energy of BLG dimerization from theoretical calculations. The experimentally determined interactions are shown to be mainly governed by electrostatic interactions and further agree with free energy calculations. Our experimental protocol aims to determine non-specific and specific interactions for a dynamically interacting system and provides an understanding of protein-protein interactions for BLG at low salt concentrations.

SIMONA 1.0: an efficient and versatile framework for stochastic simulations of molecular and nanoscale systems

Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo techniques has taken a backseat to molecular dynamics based methods, which is also reflected in the number of available simulation packages. Here, we report the development of a generic, versatile simulation package for stochastic simulations and demonstrate its application to protein conformational change, protein-protein association, small-molecule protein docking, and simulation of the growth of nanoscale clusters of organic molecules. Simulation of molecular and nanoscale systems (SIMONA) is easy to use for standard simulations via a graphical user interface and highly parallel both via MPI and the use of graphical processors. It is also extendable to many additional simulations types. Being freely available to academic users, we hope it will enable a large community of researchers in the life- and materials-sciences to use and extend SIMONA in the future. SIMONA is available for download under http://int.kit.edu/nanosim/simona.

In silico discovery of a compound with nanomolar affinity to antithrombin causing partial activation and increased heparin affinity

The medical and socioeconomic relevance of thromboembolic disorders promotes an ongoing effort to develop new anticoagulants. Heparin is widely used as activator of antithrombin but incurs side effects. We screened a large database in silico to find alternative molecules and predicted d-myo-inositol 3,4,5,6-tetrakisphosphate (TMI) to strongly interact with antithrombin. Isothermal titration calorimetry confirmed a TMI affinity of 45 nM, higher than the heparin affinity (273 nM). Functional studies, fluorescence analysis, and citrullination experiments revealed that TMI induced a partial activation of antithrombin that facilitated the interaction with heparin and low affinity heparins. TMI improved antithrombin inhibitory function of plasma from homozygous patients with antithrombin deficiency with a heparin binding defect and also in a model with endothelial cells. Our in silico screen identified a new, non-polysaccharide scaffold able to interact with the heparin binding domain of antithrombin. The functional consequences of this interaction were experimentally characterized and suggest potential anticoagulant therapeutic applications.

Independently switchable atomic quantum transistors by reversible contact reconstruction

The controlled fabrication of actively switchable atomic-scale devices, in particular transistors, has remained elusive to date. Here, we explain the operation of an atomic-scale three-terminal device by a novel switching mechanism of bistable, self-stabilizing reconstruction of the electrode contacts at the atomic level: While the device is manufactured by electrochemical deposition, it operates entirely on the basis of mechanical effects of the solid-liquid interface. We analyze mechanically and thermally stable metallic junctions with a predefined quantized conductance of 1-5 G0 in experiment and atomistic simulation. Atomistic modeling of structural and conductance properties elucidates bistable electrode reconstruction as the underlying mechanism of the device. Independent room temperature operation of two transistors at low voltage demonstrates intriguing perspectives for quantum electronics and logics on the atomic scale.

[Acute carpal tunnel syndrome in a patient with Marfan syndrome]

Acute carpal tunnel syndrome (ACTS) is rare and is mostly the result of fractures of the distal radius or the carpal bones. This paper gives the first report of an ACTS following contusion of the wrist as the result of an extensive haematoma of the flexor tendon sheath, which did not appear until 50 hours after the injury was sustained but then developed rapidly. The patient suffers from Marfan syndrome. This disease is associated with pathologic changes to the major vessels, and especially the aorta, and of the smaller peripheral vessels. It is assumed that the haematoma arose from an aneurysm of such a small vessel. The treatment of choice in ACTS is emergency incision of the carpal tunnel.

Receptor flexibility for large-scale in silico ligand screens: chances and challenges

An important contribution to today's computer-aided drug design is the automated screening of large compound databases against structurally resolved protein receptors targets. The introduction of ligand flexibility has, by now, become a standardized procedure. In contrast, a general approach to treat target degrees of freedom is still to be found, a consequence of the extreme increase of computational complexity, which comes along with the relaxation of protein degrees of freedom. In this chapter, we discuss in some detail both benefits and present limitations of target flexibility for high-throughput in silico database screens. Among the benefits are an improved diversity of binding modes, which allows one to identify a wider class of drug candidates. The limitations are related to a diminishing docking accuracy and an increased number of false hits. Using the thymidine kinase receptor and ten known inhibitors as an example, we describe in detail how target flexibility was implemented and how it affected the screening performance.

A new ligand field approach to linear transition metal dihalides

We have performed theoretical multiconfigurational calculations of the molecular energy levels based on two axial ligand field models and determined the model parameters to reproduce ab initio energies of TiCl(2), TiF(2), VCl(2), and VF(2). We develop two extensions to ligand field theory (LFT) for linear transition metal dihalides, which are incorrectly described by standard LFT. The standard LFT is augmented (1) by including the ligand induced hybridization of the d(sigma) orbital with the 4s orbital or (2) by using a different radial part for the d(sigma) orbital. Both models reproduce the energies of the first electronic states in very good agreement with numerical multireference configuration interaction results. Furthermore the model parameters are very close to experimental known Racah parameters describing the term energies of Ti(2+) and V(2+).

An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20

We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of "native content" in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence.

Basin hopping simulations for all-atom protein folding

We investigate different protocols of the basin hopping technique for de novo protein folding. Using the protein free-energy force field PFF01 we report the reproducible all-atom folding of the 20-amino-acid tryptophan-cage protein [Protein Data Bank (PDB) code: 112y] and of the recently discovered 26-amino-acid potassium channel blocker (PDB code: 1wqc), which exhibits an unusual fold. We find that simulations with increasing cycle length and random starting temperatures perform best in comparison with other parametrizations. The basin hopping technique emerges as a simple but very efficient and robust workhorse for all-atom protein folding.

Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model

A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.

Multireference calculations of the electronic structure of VF2 and VCl2

We investigated the electronic structure of two members of the transition-metal dihalide family, VF(2) and VCl(2). Using the configuration-interaction method in large basis sets we calculated the lowest 17 states of these molecules in the vicinity of their ground-state geometry. We compute the ground-state bond lengths, vibrational frequencies, and dissociation energies. In contrast to predictions of ligand-field theory, we find (4)Sigma(g) (-) ground states for both molecules.

In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

Improved implementation and application of the individually selecting configuration interaction method

We report on the progress of our implementation of the configuration-selecting multireference configuration interaction method on massively parallel architectures with distributed memory, which now permits the treatment of Hilbert spaces of dimension O(10(12)). Of these about 50,000,000 can be selected in the variational subspace. We provide scaling data for the running time of the code for the IBM/SP3 and the CRAY-T3E. We present benchmark results for two selected applications: the energetics of the isomers of dinitrosoethylene and the benchmark results for the ring closure reaction of enediyene.

An all-atom force field for tertiary structure prediction of helical proteins

We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20-60 amino acids. For each protein, decoys with 2-3 A backbone root mean-square deviation and correct experimental Cbeta-Cbeta distance constraints emerge as those with the lowest energy.

Fluctuation analysis and accuracy of a large-scalein silico screen

Using a cascadic version of the stochastic tunneling method we perform an all-atom database screen over 186,000 flexible ligands of the NCI 3D database against the thymidine kinase receptor. By analyzing the errors in the binding energy we demonstrate how the cascadic technique is superior to conventional sequential docking techniques and how reliable results for the determination of the top-scoring ligands could be achieved. The substrate corresponding to the crystal structure used in the screen ranks in the upper 0.05% of the database, validating both docking methodology and the applicability of the scoring function to this substrate. Several high ranking ligands of the database display significant structural similarity with known substrates. A detailed analysis of the accuracy of the screening method is carried out, and its dependence on the flexibility of the ligand is quantified.

All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method

All-atom protein structure prediction from the amino acid sequence alone remains an important goal of biophysical chemistry. Recent progress in force field development and validation suggests that the PFF01 free-energy force field correctly predicts the native conformation of various helical proteins as the global optimum of its free-energy surface. Reproducible protein structure prediction requires the availability of efficient optimization methods to locate the global minima of such complex potentials. Here we investigate an adapted version of the parallel tempering method as an efficient parallel stochastic optimization method for protein structure prediction. Using this approach we report the reproducible all-atom folding of the three-helix 40 amino acid HIV accessory protein from random conformations to within 2.4 A backbone RMS deviation from the experimental structure with modest computational resources.

Reproducible protein folding with the stochastic tunneling method

We report the reproducible folding of the 20 amino-acid protein trp cage using a novel version of the stochastic tunneling method and a recently developed all-atom protein free-energy force field. Six of 25 simulations reached an energy within 1 kcal/mol of the best energy, all of which correctly predicted the native experimental structure of the protein, in total eight simulations converged to the native structure. We find a strong correlation between energy and root-mean-square deviation to the native structure for all simulations.

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.

Current collapse in tunneling transport through benzene

We investigate the electrical transport through a system of benzene coupled to metal electrodes by electron tunneling. Using electronic structure calculations, a semiquantitative model for the pi electrons of the benzene is derived that includes general two-body interactions. After exact diagonalization of the benzene model the transport is computed using perturbation theory for weak electrode-benzene coupling (golden rule approximation). We include the effect of an applied electric field on the molecular states, as well as radiative relaxation. We predict a current collapse and strong negative differential conductance due to a "blocking" state when the electrode is coupled to the para-position of benzene. In contrast, for coupling to the meta-position, a series of steps in the I-V curve is found.

Disorder induced quantum phase transition in random-exchange spin-1/2 chains

We investigate the effect of quenched bond disorder on the anisotropic antiferromagnetic spin-1/2 (XXZ) chain as a model for disorder-induced quantum phase transitions. We find nonuniversal behavior of the average correlation functions for weak disorder, followed by a quantum phase transition into a strongly disordered phase with only short-range xy correlations. We find no evidence for the universal strong-disorder fixed point predicted by the real-space renormalization group, suggesting a qualitatively different view of the relationship between quantum fluctuations and disorder.

Electrical transport through single-molecule junctions: from molecular orbitals to conduction channels

We present an atomistic theory of electronic transport through single organic molecules that reproduces the important features of the current-voltage ( I-V) characteristics observed in recent experiments. We trace these features to their origin in the electronic structure of the molecules and their local atomic environment. We demonstrate how conduction channels arise from the molecular orbitals and elucidate the contributions of individual orbitals to the current. We find that in thiol-bridged aromatic molecules many molecular orbitals contribute to a single conduction channel and discuss the implications of this result for the design of molecular devices.

[Current classification of anti-arrhythmia agents]

Antiarrhythmic drugs can be divided into four Vaughan Williams classes (I-IV) according to defined electrophysiological effects on the myocardium. Thus, the Vaughan Williams classification also coincides with the main myocardial targets of the antiarrhythmics, i.e., myocardial sodium-, potassium-, and calcium-channels or beta-adrenergic receptors. A more detailed characterization which is also based on the myocardial targets of a drug is given by the "Sicilian Gambit" approach of classification. Nevertheless, the appropriate drug for the management of a given clinical arrhythmia has to be chosen according to the electrophysiological effects of the respective drug. A main determinant of the antiarrhythmic or proarrhythmic properties of a drug is the frequency dependence of its electrophysiological effects. The sodium-channel blockade induced by class-I substances is enhanced with increasing heart rates. Thus, class-I antiarrhythmics can be subclassified as substances showing a more exponential, an approximately linear, or rather saturated block-frequency relation. Class-III antiarrhythmics (potassium-channel blockade) can be further differentiated according to the component of the delayed rectifier potassium current (IK) which is inhibited by a drug. Class-III drugs inhibiting selectively the rapidly activating and deactivating IKr component exhibit a marked reverse rate dependence, i.e., the drug induced prolongation of the cardiac action potential is minimized at high rates. On the other hand, during bradycardia the pronounced action potential prolongation may cause early afterdepolarizations and triggered activity leading to torsades de pointes arrhythmias (acquired QT syndrome). Class-III substances inhibiting the slowly activating IKs component are currently under investigation and are expected to show a direct rate dependence. Experimental data available so far point to an action potential prolonging effect at least independent of rate. However, it is uncertain whether proarrhythmic effects can be thus avoided, especially in light of the fact that one form of congenital QT syndrome (LQT1) seems to be linked to dysfunction of the IKs-channel.

Replacement of dog's aorta by autologous intestinal muscle in the infected retroperitoneum

The free transplant of intestinal muscle lacking mucosa into an infected vascular bed has been shown to be a suitable replacement for the aorta in dogs. This type of transplant is incorporated into the infected area and shows a high tolerance against progressive infection. Therefore, an autologous transplant may be suitable to ensure continuous blood flow during the healing phase of a deep infection when a synthetic prosthesis is unsuccessful.

[Clinical applications of visual evoked potentials for detection of chiasmal and postchiasmal lesions (author's transl)]

Visual evoked potentials (VEP) were recorded in 18 patients with pathologic processes confirmed by computerized tomography in the chiasmal (n = 9) and parietooccipital region (n = 9). Reactions from the right and left hemisphere could be recorded separately in spite of using a simple one-channel apparatus and electrodes only at Oz and Cz. In 17 cases changes of the VEP provided information concerning the localization and extension of the lesion. In chiasmal processes we found a prolongation of monocular latencies, and a delayed or extinguished reaction to half-field stimulation from temporal retinal areas. However, the VEP was often pathologic for half-field stimulation of the nasal hemiretina. Pathologic VEPs were not always accompanied by visual field defects. In contrary to patients with chiasmal processes no pathologic reaction could be found to full-field stimulation in parieto-occipital lesions. Only when the affected hemisphere was stimulated selectively were diminution of amplitudes, prolongation of latencies, or extinguished responses observed. The VEP changes were uniform despite the cause of the lesion (tumor, ischemia). In chiasmal and parieto-occipital processes the VEP supplements computerized tomography by detecting deficits in function. This method appears suitable for monitoring the course of disease before and after neurosurgery.

'Normal' technetium bone scans in patients with acute osteomyelitis

Several investigators have stressed the usefulness of the technetium bone scan in the early diagnosis of acute osteomyelitis. Seven patients with acute osteomyelitis had initial bone scans that were reportedly normal. The diagnosis was made as a result of either an abnormal gallium scan, positive cultures, or changes in follow-up roentgenograms. The explanation for the normal technetium scans is conjectural but may be related to compromised vascularity. A normal scan does not rule out acute osteomyelitis. If this diagnosis is strongly suspected, other diagnostic tests should be used.