Nonadiabatic dynamics of cobalt tricarbonyl nitrosyl for ligand dissociation induced by electronic excitation.

We utilize real-time time-dependent density functional theory and Ehrenfest dynamics scheme to investigate excited-state nonadiabatic dynamics of ligand dissociation of cobalt tricarbonyl nitrosyl, Co(CO)NO, which is a precursor used for cobalt growth in advanced technologies, where the precursor's reaction is enhanced by electronic excitation. Based on the first-principles calculations, we demonstrate two dissociation pathways of the NO ligand on the precursor. Detailed electronic structures are further analyzed to provide an insight into dynamics following the electronic excitations.

Imaginary-Time Time-Dependent Density Functional Theory and Its Application for Robust Convergence of Electronic States.

Reliable and robust convergence to the electronic ground state within density functional theory (DFT) Kohn-Sham (KS) calculations remains a thorny issue in many systems of interest. In such cases, charge sloshing can delay or completely hinder the convergence. Here, we use an approach based on transforming the time-dependent DFT equations to imaginary time, followed by imaginary-time evolution, as a reliable alternative to the self-consistent field (SCF) procedure for determining the KS ground state.

Band alignment in quantum wells from automatically tuned DFT+U.

Band alignment between two materials is of fundamental importance for a multitude of applications. However, density functional theory (DFT) either underestimates the bandgap - as is the case with the local density approximation (LDA) or generalized gradient approximation (GGA) - or is highly computationally demanding, as is the case with hybrid-functional methods. The latter can become prohibitive in electronic-structure calculations of supercells which describe quantum wells.

Reassessing Graphene Absorption and Emission Spectroscopy.

We present a new paradigm for understanding optical absorption and hot electron dynamics experiments in graphene. Our analysis pivots on assigning proper importance to phonon-assisted indirect processes and bleaching of direct processes. We show indirect processes figure in the excess absorption in the UV region.

eReaxFF: A Pseudoclassical Treatment of Explicit Electrons within Reactive Force Field Simulations.

We present a computational tool, eReaxFF, for simulating explicit electrons within the framework of the standard ReaxFF reactive force field method. We treat electrons explicitly in a pseudoclassical manner that enables simulation several orders of magnitude faster than quantum chemistry (QC) methods, while retaining the ReaxFF transferability. We delineate here the fundamental concepts of the eReaxFF method and the integration of the Atom-condensed Kohn-Sham DFT approximated to second order (ACKS2) charge calculation scheme into the eReaxFF.

Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications.

We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials.

Anatomy of the Photochemical Reaction: Excited-State Dynamics Reveals the C-H Acidity Mechanism of Methoxy Photo-oxidation on Titania.

Light-driven chemical reactions on semiconductor surfaces have potential for addressing energy and pollution needs through efficient chemical synthesis; however, little is known about the time evolution of excited states that determine reaction pathways. Here, we study the photo-oxidation of methoxy (CH3O) derived from methanol on the rutile TiO2(110) surface using ab initio simulations to create a molecular movie of the process. The movie sequence reveals a wealth of information on the reaction intermediates, time scales, and energetics.

Preparation, applications, and digital simulation of carbon interdigitated array electrodes.

Carbon interdigitated array (IDA) electrodes with features sizes down to 1.2 μm were fabricated by controlled pyrolysis of patterned photoresist. Cyclic voltammetry of reversible redox species produced the expected steady-state currents.

Internal relaxation in dye sensitized solar cells based on Zn2SnO4 nanostructures.

In this work we study the effect of internal relaxation in a (Bu(4)N)(2)Ru(dcbpyH)(2)(NCS)(2) (N719) dye molecule in a dye sensitized solar cell. Experimentally measured light intensity dependencies of short circuit current and open circuit voltage for two different types of photoanodes, ZTO (Zn(2)SnO(4)) nanorods and nanoparticles, are explained in the framework of the proposed microscopic theory. This theory is based on a density matrix equation with a Markovian relaxation term.

Lineage-specific differences in the amino acid substitution process.

In Darwinian evolution, mutations occur approximately at random in a gene, turned into amino acid mutations by the genetic code. Some mutations are fixed to become substitutions and some are eliminated from the population. Partitioning pairs of closely related species with complete genome sequences by average population size of each pair, we looked at the substitution matrices generated for these partitions and compared the substitution patterns between species.

Using evolutionary information to find specificity-determining and co-evolving residues.

Intricate networks of protein interactions rely on the ability of a protein to recognize its targets: other proteins, ligands, and sites on DNA and RNA. To recognize other molecules, it was suggested that a protein uses a small set of specificity-determining residues (SDRs). How can one find these residues in proteins and distinguish them from other functionally important amino acids? A number of bioinformatics methods to predict SDRs have been developed in recent years.

Complex microsatellite dynamics in the myostatin gene within ruminants.

A microsatellite has previously been identified in myostatin in cattle. Sequencing of this region from other artiodactyls coupled with phylogenetic analysis has been used to uncover the potential origins of the microsatellite event, which appears either to have been born twice or to have been gained and lost within ruminants. While caprids and ovids share the ancestral state with pigs and other mammals, microsatellite activity (length polymorphism) is uncovered in both deer and bovids.

How gene order is influenced by the biophysics of transcription regulation.

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure.

Protein knot server: detection of knots in protein structures.

KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures.

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.

The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized 'hypothetical' genes. These genes, which have not been experimentally characterized and whose functions cannot be deduced from simple sequence comparisons alone, now comprise a significant fraction of the public databases. Expression analyses of Haemophilus influenzae cells using a combination of transcriptomic and proteomic approaches resulted in confident identification of 54 'hypothetical' genes that were expressed in cells under normal growth conditions.

Phylogenetic web profiler.

Phylogenetic Web Profiler (PWP) is a web-based service designed to perform phylogenetic profiling of proteins against genomes. The current version offers a selection of 63 completed genomes and available plasmids as annotated in the PEDANT genome database. Unlike currently available applications, this tool offers several choices of ortholog prediction parameters including E-value cutoff, percent length difference tolerance, and annotation similarity.

The PEDANT genome database.

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface.

SNAPper: gene order predicts gene function.

Unlabelled: SNAPper is a network service for predicting gene function based on the conservation of gene order.

Availability: The SNAPper server is available at http://pedant.gsf.

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome.

Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant.