Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential VA on a one-atom density ρ A or ρ B. To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale

Vertically coupled double quantum rings at zero magnetic field

Within local-spin-density functional theory, we have investigated the ¿dissociation¿ of few-electron circular vertical semiconductor double quantum ring artificial molecules at zero magnetic field as a function of interring distance. In a first step, the molecules are constituted by two identical quantum rings. When the rings are quantum mechanically strongly coupled, the electronic states are substantially delocalized, and the addition energy spectra of the artificial molecule resemble those of a single quantum ring in the few-electron limit. When the rings are quantum mechanically weakly coupled, the electronic states in the molecule are substantially localized in one ring or the other, although the rings can be electrostatically coupled. The effect of a slight mismatch introduced in the molecules from nominally identical quantum wells, or from changes in the inner radius of the constituent rings, induces localization by offsetting the energy levels in the quantum rings. This plays a crucial role in the appearance of the addition spectra as a function of coupling strength particularly in the weak coupling limit.

Nonrelativistic bound states at finite temperature. II. Muonic hydrogen

We illustrate how to apply modern effective field-theory techniques and dimensional regularization to factorize the various scales, which appear in QED bound states at finite temperature. We focus here on the muonic hydrogen atom. Vacuum polarization effects make the physics of this atom at finite temperature very close to that of heavy quarkonium states. We comment on the implications of our results for these states in the quark gluon plasma. In particular, we estimate the effects of a finite-charm quark mass in the dissociation temperature of bottomonium.

Calorimetry of hydrogen desorption from a-Si nanoparticles

The process of hydrogen desorption from amorphous silicon (a-Si) nanoparticles grown by plasma-enhanced chemical vapor deposition (PECVD) has been analyzed by differential scanning calorimetry (DSC), mass spectrometry, and infrared spectroscopy, with the aim of quantifying the energy exchanged. Two exothermic peaks centered at 330 and 410 C have been detected with energies per H atom of about 50 meV. This value has been compared with the results of theoretical calculations and is found to agree with the dissociation energy of Si-H groups of about 3.25 eV per H atom, provided that the formation energy per dangling bond in a-Si is about 1.15 eV. It is shown that this result is valid for a-Si:H films, too.

Counter-ion effect on surfactant-DNA gel particles as controlled DNA delivery systems

The ability to entrap drugs within vehicles and subsequently release them has led to new treatments for a number of diseases. Based on an associative phase separation and interfacial diffusion approach, we developed a way to prepare DNA gel particles without adding any kind of cross-linker or organic solvent. Among the various agents studied, cationic surfactants offered particularly efficient control for encapsulation and DNA release from these DNA gel particles. The driving force for this strong association is the electrostatic interaction between the two components, as induced by the entropic increase due to the release of the respective counter-ions. However, little is known about the influence of the respective counter-ions on this surfactant-DNA interaction. Here we examined the effect of different counter-ions on the formation and properties of the DNA gel particles by mixing DNA (either single- (ssDNA) or double-stranded (dsDNA)) with the single chain surfactant dodecyltrimethylammonium (DTA). In particular, we used as counter-ions of this surfactant the hydrogen sulfate and trifluoromethane sulfonate anions and the two halides, chloride and bromide. Effects on the morphology of the particles obtained, the encapsulation of DNA and its release, as well as the haemocompatibility of these particles, are presented, using the counter-ion structure and the DNA conformation as controlling parameters. Analysis of the data indicates that the degree of counter-ion dissociation from the surfactant micelles and the polar/hydrophobic character of the counter-ion are important parameters in the final properties of the particles. The stronger interaction with amphiphiles for ssDNA than for dsDNA suggests the important role of hydrophobic interactions in DNA.

Performance of correlation functionals in ab initio chemisorption cluster-model calculations: Alkali metals on Si(111)

The performance of different correlation functionals has been tested for alkali metals, Li to Cs, interacting with cluster models simulating different active sites of the Si(111) surface. In all cases, the ab initio Hartree-Fock density has been obtained and used as a starting point. The electronic correlation energy is then introduced as an a posteriori correction to the Hartree-Fock energy using different correlation functionals. By making use of the ionic nature of the interaction and of different dissociation limits we have been able to prove that all functionals tested introduce the right correlation energy, although to a different extent. Hence, correlation functionals appear as an effective and easy way to introduce electronic correlation in the ab initio Hartree-Fock description of the chemisorption bond in complex systems where conventional configuration interaction techniques cannot be used. However, the calculated energies may differ by some tens of eV. Therefore, these methods can be employed to get a qualitative idea of how important correlation effects are, but they have some limitations if accurate binding energies are to be obtained.

Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling

Phototransduction in vertebrate photoreceptor cells represents a paradigm of signaling pathways mediated by G-protein-coupled receptors (GPCRs), which share common modules linking the initiation of the cascade to the final response of the cell. In this work, we focused on the recovery phase of the visual photoresponse, which is comprised of several interacting mechanisms. We employed current biochemical knowledge to investigate the response mechanisms of a comprehensive model of the visual phototransduction pathway. In particular, we have improved the model by implementing a more detailed representation of the recoverin (Rec)-mediated calcium feedback on rhodopsin kinase and including a dynamic arrestin (Arr) oligomerization mechanism. The model was successfully employed to investigate the rate limiting steps in the recovery of the rod photoreceptor cell after illumination. Simulation of experimental conditions in which the expression levels of rhodospin kinase (RK), of the regulator of the G-protein signaling (RGS), of Arr and of Rec were altered individually or in combination revealed severe kinetic constraints to the dynamics of the overall network. Our simulations confirm that RGS-mediated effector shutdown is the rate-limiting step in the recovery of the photoreceptor and show that the dynamic formation and dissociation of Arr homodimers and homotetramers at different light intensities significantly affect the timing of rhodopsin shutdown. The transition of Arr from its oligomeric storage forms to its monomeric form serves to temper its availability in the functional state. Our results may explain the puzzling evidence that overexpressing RK does not influence the saturation time of rod cells at bright light stimuli. The approach presented here could be extended to the study of other GPCR signaling pathways.

Nanoparticles in SiH4-Ar plasma: Modelling and comparison with experimental data

Experimental and theoretical investigations for growth of silicon nanoparticles (4 to 14 nm) in radio frequency discharge were carried out. Growth processes were performed with gas mixtures of SiH4 and Ar in a plasma chemical reactor at low pressure. A distinctive feature of presented kinetic model of generation and growth of nanoparticles (compared to our earlier model) is its ability to investigate small"critical" dimensions of clusters, determining the rate of particle production and taking into account the influence of SiH2 and Si2Hm dimer radicals. The experiments in the present study were extended to high pressure (≥20 Pa) and discharge power (≥40 W). Model calculations were compared to experimental measurements, investigating the dimension of silicon nanoparticles as a function of time, discharge power, gas mixture, total pressure, and gas flow.

A semi-grand canonical Monte Carlo simulation model for ion binding to ionizable surfaces: proton binding of carboxylated latex particles as a case study

In this paper, we present a computer simulation study of the ion binding process at an ionizable surface using a semi-grand canonical Monte Carlo method that models the surface as a discrete distribution of charged and neutral functional groups in equilibrium with explicit ions modelled in the context of the primitive model. The parameters of the simulation model were tuned and checked by comparison with experimental titrations of carboxylated latex particles in the presence of different ionic strengths of monovalent ions. The titration of these particles was analysed by calculating the degree of dissociation of the latex functional groups vs. pH curves at different background salt concentrations. As the charge of the titrated surface changes during the simulation, a procedure to keep the electroneutrality of the system is required. Here, two approaches are used with the choice depending on the ion selected to maintain electroneutrality: counterion or coion procedures. We compare and discuss the difference between the procedures. The simulations also provided a microscopic description of the electrostatic double layer (EDL) structure as a function of p H and ionic strength. The results allow us to quantify the effect of the size of the background salt ions and of the surface functional groups on the degree of dissociation. The non-homogeneous structure of the EDL was revealed by plotting the counterion density profiles around charged and neutral surface functional groups.

A semi-grand canonical Monte Carlo simulation model for ion binding to ionizable surfaces: Proton binding of carboxylated latex particles as a case study

In this paper, we present a computer simulation study of the ion binding process at an ionizable surface using a semi-grand canonical Monte Carlo method that models the surface as a discrete distribution of charged and neutral functional groups in equilibrium with explicit ions modelled in the context of the primitive model. The parameters of the simulation model were tuned and checked by comparison with experimental titrations of carboxylated latex particles in the presence of different ionic strengths of monovalent ions. The titration of these particles was analysed by calculating the degree of dissociation of the latex functional groups vs. pH curves at different background salt concentrations. As the charge of the titrated surface changes during the simulation, a procedure to keep the electroneutrality of the system is required. Here, two approaches are used with the choice depending on the ion selected to maintain electroneutrality: counterion or coion procedures. We compare and discuss the difference between the procedures. The simulations also provided a microscopic description of the electrostatic double layer (EDL) structure as a function of pH and ionic strength. The results allow us to quantify the effect of the size of the background salt ions and of the surface functional groups on the degree of dissociation. The non-homogeneous structure of the EDL was revealed by plotting the counterion density profiles around charged and neutral surface functional groups. © 2011 American Institute of Physics.

Classical line shapes based on analytical solutions of bimolecular trajectories in collision induced emission. II. Reactive collisions

The classical theory of collision induced emission (CIE) from pairs of dissimilar rare gas atoms was developed in Paper I [D. Reguera and G. Birnbaum, J. Chem. Phys. 125, 184304 (2006)] from a knowledge of the straight line collision trajectory and the assumption that the magnitude of the dipole could be represented by an exponential function of the inter-nuclear distance. This theory is extended here to deal with other functional forms of the induced dipole as revealed by ab initio calculations. Accurate analytical expression for the CIE can be obtained by least square fitting of the ab initio values of the dipole as a function of inter-atomic separation using a sum of exponentials and then proceeding as in Paper I. However, we also show how the multi-exponential fit can be replaced by a simpler fit using only two analytic functions. Our analysis is applied to the polar molecules HF and HBr. Unlike the rare gas atoms considered previously, these atomic pairs form stable bound diatomic molecules. We show that, interestingly, the spectra of these reactive molecules are characterized by the presence of multiple peaks. We also discuss the CIE arising from half collisions in excited electronic states, which in principle could be probed in photo-dissociation experiments.

Brain dynamics sustaining rapid rule extraction from speech

Language acquisition is a complex process that requires the synergic involvement of different cognitive functions, which include extracting and storing the words of the language and their embedded rules for progressive acquisition of grammatical information. As has been shown in other fields that study learning processes, synchronization mechanisms between neuronal assemblies might have a key role during language learning. In particular, studying these dynamics may help uncover whether different oscillatory patterns sustain more item-based learning of words and rule-based learning from speech input. Therefore, we tracked the modulation of oscillatory neural activity during the initial exposure to an artificial language, which contained embedded rules. We analyzed both spectral power variations, as a measure of local neuronal ensemble synchronization, as well as phase coherence patterns, as an index of the long-range coordination of these local groups of neurons. Synchronized activity in the gamma band (2040 Hz), previously reported to be related to the engagement of selective attention, showed a clear dissociation of local power and phase coherence between distant regions. In this frequency range, local synchrony characterized the subjects who were focused on word identification and was accompanied by increased coherence in the theta band (48 Hz). Only those subjects who were able to learn the embedded rules showed increased gamma band phase coherence between frontal, temporal, and parietal regions.

Calorimetry of hydrogen desorption from ɑ-Si nanoparticles

The process of hydrogen desorption from amorphous silicon (ɑ-Si) nanoparticles grown by plasmaenhanced chemical vapor deposition (PECVD) has been analyzed by differential scanning calorimetry (DSC), mass spectrometry, and infrared spectroscopy, with the aim of quantifying the energy exchanged. Two exothermic peaks centered at 330 and 410 °C have been detected with energies per H atom of about 50 meV. This value has been compared with the results of theoretical calculations and is found to agree with the dissociation energy of Si-H groups of about 3.25 eV per H atom, provided that the formation energy per dangling bond in ɑ-Si is about 1.15 eV. It is shown that this result is valid for ɑ-Si:H films, too