Molecular dynamics simulation on the complex of the tobramycin and 16S rRNA a site

A 3. 6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two l

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

Electron dynamics and harmonics emission spectra due to electron oscillation driven by intense laser pulses

The dynamics and harmonics emission spectra due to electron oscillation driven by intense laser pulses have been investigated considering a single electron model. The spectral and angular distributions of the harmonics radiation are numerically analyzed and demonstrate significantly different characteristics from those of the low-intensity field case. Higher-order harmonic radiation is possible for a sufficiently intense driving laser pulse. A complex shifting and broadening structure of the spectrum is observed and analyzed for different polarization. For a realistic pulsed photon beam, the spectrum of the radiation is redshifted for backward radiation and blueshifted for forward radiation, and spectral broadening is noticed. This is due to the changes in the longitudinal velocity of the electron during the laser pulse. These effects are much more pronounced at higher laser intensities giving rise to even higher-order harmonics that eventually leads to a continuous spectrum. Numerical simulations have further shown that broadening of the high harmonic radiation can be limited by increasing the laser pulse width. The complex shifting and broadening of the spectra can be employed to characterize the ultrashort and ultraintense laser pulses and to study the ultrafast dynamics of the electrons. (c) 2006 American Institute of Physics.

Dynamics of femtosecond laser pulse induced damage in multilayers

We report the single-shot damage thresholds of MgF2/ZnS onmidirectional reflector for laser pulse durations from 50 A to 900 fs. A coupled dynamic model is applied to study the damage mechanisms, in which we consider not only the electronic excitation of the material, but also the influence of this excitation-induced changes in the complex refractive index of material on the laser pulse itself. The results indicate that this feedback effect plays a very important role during the damage of material. Based on this model, we calculate the threshold fluences and the time-resolved excitation process of the multiplayer. The theoretical calculations agree well with our experimental results. (c) 2005 Elsevier B.V. All rights reserved.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Complex mutation at a microsatellite locus in sturgeons: Acipenser sinensis, A-schrenckii, A-gueldenstaedtii and A-baerii

Cross-species amplifications of microsatellite locus Spl-106, which was originally screened from the genome of shovelnose sturgeon (Scaphirhynchus platorynchus) with a perfect TAGA repeat motif, were carried out in four other species of the genera Acipenser. A total of 34 polymerase chain reaction (PCR) products representing 16 different alleles of this locus was sequenced. Sequence analysis results showed that besides the number changes of repeat units, many mutational events, such as single-base substitutions and various insertion/deletion (indels) occurred not only at species level but also at individual level, even among the different alleles within the same individual. The repeat motifs varied from perfect (TAGA)n array to perfect compound (TAAA)m (GAAA)n and perfect or imperfect compound (TAAA)m (TAGA)n (TAAA)x arrays in different species and different individuals. The evolution dynamics of this locus in sturgeons was inferred in that it may evolve from a single perfect to different perfect or imperfect compounds.

Nutrient dynamics and the eutrophication of shallow lakes Kasumigaura (Japan), Donghu (PR China), and Okeechobee (USA)

We compared the nutrient dynamics of three lakes that have been heavily influenced by point and non-point source pollution and other human activities. The lakes, located in Japan (Lake Kasumigaura), People's Republic of China (Lake Donghu), and the USA (Lake Okeechobee), all are relatively large(>30 km(2)), very shallow (<4 m mean depth), and eutrophic. In all three lakes we found strong interactions among the sediments, water column, and human activities. Important processes affecting nutrient dynamics included nitrogen fixation, light limitation due to resuspended sediments, and intense grazing on algae by cultured fish. As a result of these complex interactions, simple empirical models developed to predict in-lake responses of total phosphorus and algal biomass to external nutrient loads must be used with caution. While published models may provide 'good' results, in terms of model output matching actual data, this may not be due to accurate representation of lake processes in the models. The variable nutrient dynamics that we observed among the three study lakes appears to be typical for shallow lake systems. This indicates that a greater reliance on lake-specific research may be required for effective management, and a lesser role of inter-lake generalization than is possible for deeper, dimictic lake systems. Furthermore, accurate predictions of management impacts in shallow eutrophic lakes may require the use of relatively complex deterministic modeling tools. (C) 2000 Elsevier Science Ltd. All rights reserved.

Dynamics of quantum dissipation systems interacting with fermion and boson grand canonical bath ensembles: Hierarchical equations of motion approach

A hierarchical equations of motion formalism for a quantum dissipation system in a grand canonical bath ensemble surrounding is constructed on the basis of the calculus-on-path-integral algorithm, together with the parametrization of arbitrary non-Markovian bath that satisfies fluctuation-dissipation theorem. The influence functionals for both the fermion or boson bath interaction are found to be of the same path integral expression as the canonical bath, assuming they all satisfy the Gaussian statistics. However, the equation of motion formalism is different due to the fluctuation-dissipation theories that are distinct and used explicitly. The implications of the present work to quantum transport through molecular wires and electron transfer in complex molecular systems are discussed. (c) 2007 American Institute of Physics.

Bubble Dynamics and Heat Transfer in Microgravity Pool Boiling

Boiling is an extremely complicated and illusive process. Microgravity experiments offer a unique opportunity to study the complex interactions without external forces, such as buoyancy, which can affect the bubble dynamics and the related heat transfer. Furthermore, they can also provide a means to study the actual influence of gravity on the boiling. Two research projects on pool boiling in microgravity have been conducted aboard the Chinese recoverable satellites. Ground-based experiments both in normal gravity and in short-term microgravity in the Drop Tower Beijing and numerical simulations have also been performed. Steady boiling of R113 on thin platinum wires was studied with a temperature-controlled heating method, while quasi-steady boiling of FC-72 on a plane plate was investigated with an exponentially increasing heating voltage. It was found that the bubble dynamics in microgravity has a distinct difference from that in normal gravity, and that the heat transfer characteristic is depended upon the bubble dynamics. Lateral motions of bubbles on the heaters were observed before their departure in microgravity. The surface oscillation of the merged bubbles due to lateral coalescence between adjacent bubbles drove it to detach from the heaters. Slight enhancement of heat transfer on wires is observed in microgravity, while diminution is evident for high heat flux in the plate case.

Efficiency Dynamics on Two Coupled Small-World Networks

We investigate the effect of clusters in complex networks on efficiency dynamics by studying a simple efficiency model in two coupled small-world networks. It is shown that the critical network randomness corresponding to transition from a stagnant phase to a growing one decreases to zero as the connection strength of clusters increases. It is also shown for fixed randomness that the state of clusters transits from a stagnant phase to a growing one as the connection strength of clusters increases. This work can be useful for understanding the critical transition appearing in many dynamic processes on the cluster networks.

EFFICIENCY DYNAMICS ON SCALE-FREE NETWORKS WITH COMMUNITIES

The simple efficiency model is developed on scale-free networks with communities to study the effect of the communities in complex networks on efficiency dynamics. For some parameters, we found that the state of system will transit from a stagnant phase to a growing phase as the strength of community decreases.

The optical properties and the natural lifetime calculation of a Sm(III) complex

The photophysical properties of the complex Sm(PM)(3)(TP)(2) [PM = 1-phenyl-3-methyl-4-isobutyryl-5-pyrazolone, TP = triphenyl phosphine oxide] are determined in crystal state, and energy transfer process is modeled for ligands to center Sm(III) ion. The characteristic luminescence of Sm(III) is sensitized by PM and TP, and most of transitions from excited state (4)G(5/2) of Sm3+ are detected.

Four New Lanthanide-Nitronyl Nitroxide (Ln(III)=Pr-III, Sm-III, Eu-III, Tm-III) Complexes and a Tb-III Complex Exhibiting Single-Molecule Magnet Behavior

Five new complexes based on rare-earth-radical [Ln(hfac)(3)(NIT-5-Br-3py)](2) (Ln=Pr (1), Sm (2), Eu (3), Tb (4), Tm (5); hfac = hexafluoroacetylacetonate; NIT-5-Br-3py = 2-(4,4,5,5-tetramethyl-3-oxylimidazoline-1-oxide)-5-bromo-3-pyridine) have been synthesized and characterized by X-ray crystal diffraction. The single-crystal structures show that these complexes have similar structures, in which a NIT-5-Br-3py molecule acts as a bridging ligand linking two Ln(III) ions through the oxygen atom of the N-O group and nitrogen atom from the pyridine ring to form a four-spin system. Both static and dynamic magnetic properties were measured for complex 4, which exhibits single-molecule magnetism behavior.

The complex kinetics of protein folding in wide temperature ranges

The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T-0 is found to be smaller than the folding transition temperature T-f. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly nonexponential kinetics. The transition temperature is at T-k and T-0, T-k, T-f. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures ( lower than trapping transition temperature T< T-0/(4&SIM;6)), the kinetics is an exponential Poissonian process again.