Diffusion of intruders in granular suspensions: Enskog theory and random walk interpretation.

The Enskog kinetic theory is applied to compute the mean square displacement of impurities or intruders (modeled as smooth inelastic hard spheres) immersed in a granular gas of smooth inelastic hard spheres (grains). Both species (intruders and grains) are surrounded by an interstitial molecular gas (background) that plays the role of a thermal bath. The influence of the latter on the motion of intruders and grains is modeled via a standard viscous drag force supplemented by a stochastic Langevin-like force proportional to the background temperature.

Topographic effects on dispersal patterns of Phytophthora cinnamomi at a stand scale in a Spanish heathland.

Phytophthora cinnamomi is one of the most important plant pathogens in the world, causing root rot in more than a thousand plant species. This observational study was carried out on a P. cinnamomi infected heathland of Erica umbellata used as goat pasture.

Tuning the Electronic and Dynamical Properties of a Molecule by Atom Trapping Chemistry.

The ability to trap adatoms with an organic molecule on a surface has been used to obtain a range of molecular functionalities controlled by the choice of the molecular trapping site and local deprotonation. The tetraphenylporphyrin molecule used in this study contains three types of trapping sites: two carbon rings (phenyl and pyrrole) and the center of a macrocycle. Catching a gold adatom on the carbon rings leads to an electronic doping of the molecule, whereas trapping the adatom at the macrocycle center with single deprotonation leads to a molecular rotor and a second deprotonation leads to a molecular jumper.

Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems.

Influence of the environment on the oxidative deamination of p-substituted benzylamines in monoamine oxidase.

The flavin-containing enzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of amine neurotransmitters. The exact mechanism of the oxidative deamination of amines to aldehydes by the enzyme has not yet been fully understood despite extensive research on the area. The rate limiting step is the reductive half-reaction where the Hα together with two electrons of the amine substrate is transferred to the flavin cofactor.

Lattice statistical theory of random walks on a fractal-like geometry.

We have designed a two-dimensional, fractal-like lattice and explored, both numerically and analytically, the differences between random walks on this lattice and a regular, square-planar Euclidean lattice. We study the efficiency of diffusion-controlled processes for flows from external sites to a centrosymmetric reaction center and, conversely, for flows from a centrosymmetric source to boundary sites. In both cases, we find that analytic expressions derived for the mean walk length on the fractal-like lattice have an algebraic dependence on system size, whereas for regular Euclidean lattices the dependence can be transcendental.

Reaction mechanism of the bicopper enzyme peptidylglycine α-hydroxylating monooxygenase.

Peptidylglycine α-hydroxylating monooxygenase is a noninteracting bicopper enzyme that stereospecifically hydroxylates the terminal glycine of small peptides for its later amidation. Neuroendocrine messengers, such as oxytocin, rely on the biological activity of this enzyme. Each catalytic turnover requires one oxygen molecule, two protons from the solvent, and two electrons.

Nonadiabatic Ensemble Simulations of cis-Stilbene and cis-Azobenzene Photoisomerization.

Structurally, stilbene and azobenzene molecules exist in closed and open cis and trans forms, which are able to transform into each other under the influence of light (photoisomerization). To accurately simulate the photoisomerization processes, one must go beyond ground-state (Born-Oppenheimer) calculations and include nonadiabatic coupling between the electronic and vibrational states. We have successfully implemented nonadiabatic couplings and a surface-hopping algorithm within a density functional theory approach that utilizes local orbitals.

Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels.

Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF).

Barrier height formation in organic blends/metal interfaces: case of tetrathiafulvalene-tetracyanoquinodimethane/Au(111).

The interface between the tetrathiafulvalene/tetracyanoquinodimethane (TTF-TCNQ) organic blend and the Au(111) metal surface is analyzed by Density Functional Theory calculations, including the effect of the charging energies on the molecule transport gaps. Given the strong donor and acceptor characters of the TTF and TCNQ molecules, respectively, there is a strong intermolecular interaction, with a relatively high charge transfer between the two organic materials, and between the organic layer and the metal surface. We find that the TCNQ LUMO peak is very close to the Fermi level; due to the interaction with the metal surface, the organic molecular levels are broadened, creating an important induced density of interface states (IDIS).

Reaction mechanism of monoamine oxidase from QM/MM calculations.

The flavoenzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of neurotransmitters. While it is commonly accepted that the rate limiting step of the reaction is the stereoselective abstraction of a hydrogen from the substrate, the precise mechanism is unknown. We modeled the reaction of human MAO-B with benzylamine by means of QM/MM calculations based on density functional theory.

Detailed Examination of a Single Conduction Event in a Potassium Channel.

Although extensively studied, it has proved difficult to describe in detail how potassium ion channels conduct cations and water. We present a computational study that, by using stratified umbrella sampling, examines nearly an entire conduction event of the Kv1.2/2.

Calculation of non-adiabatic coupling vectors in a local-orbital basis set.

Most of today's molecular-dynamics simulations of materials are based on the Born-Oppenheimer approximation. There are many cases, however, in which the coupling of the electrons and nuclei is important and it is necessary to go beyond the Born-Oppenheimer approximation. In these methods, the non-adiabatic coupling vectors are fundamental since they represent the link between the classical atomic motion of the nuclei and the time evolution of the quantum electronic state.

Narrow escape time to a structured target located on the boundary of a microdomain.

The forward binding rate of chemical reactions is the reciprocal of the mean time for a Brownian molecule to hit its molecular target. When the target is embedded in the surface of a microdomain, this time is known as the narrow escape time, and it has been computed for various geometries. However, for large targets that extend from the surface far into the cytosol the classical computations do not apply and new ones are needed.