Dynamical Properties and Plasmon Dispersion of a Weakly Degenerate Correlated One-Component Plasma

Classical Molecular Dynamics (MD) simulations for a one-component plasma (OCP) are presented. Quantum effects are included in the form of the Kelbg potential. Results for the dynamical structure factor are compared with the Vlasov and RPA (random phase approximation) theories. The influence of the coupling parameter $\Gamma$, degeneracy parameter $\rho \Lambda^3$ and the form of the pair interaction on the optical plasmon dispersion is investigated. An improved analytical approximation for the dispersion of Langmuir waves is presented.Comment: 23 pages, includes 7 ps/eps-figures and 2 table

An orbital-free molecular dynamics study of melting in K_20, K_55, K_92, K_142, Rb_55 and Cs_55 clusters

The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behavior of Na_55 and K_55. As the atomic number increases, the height of the specific heat peaks decreases, their width increases, and the melting temperature decreases as in bulk melting, but in a more pronounced way.Comment: LaTeX file. 6 pages with 17 pictures. Final version with minor change

Variational Approach to Molecular Kinetics

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics

Atomic-scale modeling of the deformation of nanocrystalline metals

Nanocrystalline metals, i.e. metals with grain sizes from 5 to 50 nm, display technologically interesting properties, such as dramatically increased hardness, increasing with decreasing grain size. Due to the small grain size, direct atomic-scale simulations of plastic deformation of these materials are possible, as such a polycrystalline system can be modeled with the computational resources available today. We present molecular dynamics simulations of nanocrystalline copper with grain sizes up to 13 nm. Two different deformation mechanisms are active, one is deformation through the motion of dislocations, the other is sliding in the grain boundaries. At the grain sizes studied here the latter dominates, leading to a softening as the grain size is reduced. This implies that there is an ``optimal'' grain size, where the hardness is maximal. Since the grain boundaries participate actively in the deformation, it is interesting to study the effects of introducing impurity atoms in the grain boundaries. We study how silver atoms in the grain boundaries influence the mechanical properties of nanocrystalline copper.Comment: 10 pages, LaTeX2e, PS figures and sty files included. To appear in Mater. Res. Soc. Symp. Proc. vol 538 (invited paper). For related papers, see http://www.fysik.dtu.dk/~schiotz/publist.htm

In Vitro Dedifferentiation of Melanocytes from Adult Epidermis

In previous work we described a novel culture technique using a cholera toxin and PMA-free medium (Mel-mix) for obtaining pure melanocyte cultures from human adult epidermis. In Mel-mix medium the cultured melanocytes are bipolar, unpigmented and highly proliferative. Further characterization of the cultured melanocytes revealed the disappearance of c-Kit and TRP-1 and induction of nestin expression, indicating that melanocytes dedifferentiated in this in vitro culture. Cholera toxin and PMA were able to induce c-Kit and TRP-1 protein expressions in the cells, reversing dedifferentiation. TRP-1 mRNA expression was induced in dedifferentiated melanocytes by UV-B irradiated keratinocyte supernatants, however direct UV-B irradiation of the cells resulted in further decrease of TRP-1 mRNA expression. These dedifferentiated, easily accessible cultured melanocytes provide a good model for studying melanocyte differentiation and possibly transdifferentiation. Because melanocytes in Mel-mix medium can be cultured with human serum as the only supplement, this culture system is also suitable for autologous cell transplantation

The Free Energy Landscape of Small Molecule Unbinding

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding

Acute Stress Induces Contrasting Changes in AMPA Receptor Subunit Phosphorylation within the Prefrontal Cortex, Amygdala and Hippocampus

Exposure to stress causes differential neural modifications in various limbic regions, namely the prefrontal cortex, hippocampus and amygdala. We investigated whether α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) phosphorylation is involved with these stress effects. Using an acute inescapable stress protocol with rats, we found opposite effects on AMPA receptor phosphorylation in the medial prefrontal cortex (mPFC) and dorsal hippocampus (DH) compared to the amygdala and ventral hippocampus (VH). After stress, the phosphorylation of Ser831-GluA1 was markedly decreased in the mPFC and DH, whereas the phosphorylation of Ser845-GluA1 was increased in the amygdala and VH. Stress also modulated the GluA2 subunit with a decrease in the phosphorylation of both Tyr876-GluA2 and Ser880-GluA2 residues in the amygdala, and an increase in the phosphorylation of Ser880-GluA2 in the mPFC. These results demonstrate that exposure to acute stress causes subunit-specific and region-specific changes in glutamatergic transmission, which likely lead to the reduced synaptic efficacy in the mPFC and DH and augmented activity in the amygdala and VH. In addition, these findings suggest that modifications of glutamate receptor phosphorylation could mediate the disruptive effects of stress on cognition. They also provide a means to reconcile the contrasting effects that stress has on synaptic plasticity in these regions. Taken together, the results provide support for a brain region-oriented approach to therapeutics

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p