Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

Differential dynamics of the serotonin(1A) receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation

The serotonin(1A) receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin(1A) receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3s, to analyze the effect of cholesterol on the structure and dynamics of the serotonin(1A) receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin(1A) receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.

Insight into the Evaporation Dynamics of a Pair of Sessile Droplets on a Hydrophobic Substrate

In this work, we have demonstrated three unique regimes in the evaporation lifecycle of a pair of sessile droplets placed in variable proximity on a hydrophobic substrate. For small separation distance, the droplets undergo asymmetric spatiotemporal,evaporation leading to contact angle hysteresis and suppressed vaporization. The reduced evaporation has been attributed quantitatively to the existence of a constrained vapor-rich dome between the two droplets. However, a dynamic decrease in the droplet radius due to solvent removal marks a return to symmetry in terms of evaporation and contact angle. We have described the variation in evaporation flux using a universal correction factor. We have also demonstrated the existence of a critical separation distance beyond which the droplets in the, droplet pair do not affect each other. The results are crucial to a plethora of applications ranging from surface patterning to lab-on-a-chip devices.

Nanomechanical Mapping, Hierarchical Polymer Dynamics, and Miscibility in the Presence of Chain-End Grafted Nanoparticles

To improve the spatial distribution of nano particles in a polymeric host and to enhance the interfacial interaction with the host, the use of chain-end grafted nanoparticle has gained popularity in the field of polymeric nanocomposites. Besides changing the material properties of the host, these grafted nanoparticles strongly alter the dynamics of the polymer chain at both local and cooperative length scales (relaxations) by manipulating the enthalpic and entropic interactions. It is difficult to map the distribution of these chain-end grafted nanoparticles in the blend by conventional techniques, and herein, we attempted to characterize it by unique technique(s) like peak force quantitative nanomechanical mapping (PFQNM) through AFM (atomic force microscopy) imaging and dielectric relaxation spectroscopy (DRS). Such techniques, besides shedding light on the spatial distribution of the nanoparticles, also give critical information on the changing elasticity at smaller length scales and hierarchical polymer chain dynamics in the vicinity of the nanoparticles. The effect of one-dimensional rodlike multiwall carbon nanotubes (MWNTs), with the characteristic dimension of the order of the radius of gyration of the polymeric chain, on the phase miscibility and chain dynamics in a classical LCST mixture of polystyrene/ poly(vinyl methyl ether) (PS/PVME) was examined in detail using the above techniques. In order to tune the localization of the nanotubes, different molecular weights of PS (13, 31, and 46 kDa), synthesized using RAFT (reversible addition fragmentation chain transfer) polymerization, was grafted onto MWNTs in situ. The thermodynamic miscibility in the blends was assessed by low-amplitude isochronal temperature sweeps, the spatial distribution of MWNTs in the blends was evaluated by PFQNM, and the hierarchical polymer chain dynamics was studied by DRS. It was observed that the miscibility, concentration fluctuation, and cooperative relaxations of the PS/PVME blends are strongly governed by the spatial distribution of MWNTs in the blends. These findings should help guide theories and simulations of hierarchical chain dynamics in LCST mixtures containing rodlike nanoparticles.

Quasi-geostrophic dynamics in the presence of moisture gradients

The derivation of a quasi-geostrophic system from the rotating shallow-water equations on a midlatitude -plane coupled with moisture is presented. Condensation is prescribed to occur whenever the moisture at a point exceeds a prescribed saturation value. It is seen that a slow condensation time-scale is required to obtain a consistent set of equations at leading order. Further, since the advecting wind fields are geostrophic, changes in moisture (and hence precipitation) occur only via non-divergent mechanisms. Following observations, a saturation profile with gradients in the zonal and meridional directions is prescribed. A purely meridional gradient has the effect of slowing down the dry Rossby waves, through a reduction in the equivalent gradient' of the background potential vorticity. A large-scale unstable moist mode results on the inclusion of a zonal gradient by itself, or in conjunction with a meridional moisture gradient. For gradients that are are representative of the atmosphere, the most unstable moist mode propagates zonally in the direction of increasing moisture, matures over an intraseasonal time-scale and has small phase speed.

Insight into the Evaporation Dynamics of a Pair of Sessile Droplets on a Hydrophobic Substrate

In this work, we have demonstrated three unique regimes in the evaporation lifecycle of a pair of sessile droplets placed in variable proximity on a hydrophobic substrate. For small separation distance, the droplets undergo asymmetric spatiotemporal,evaporation leading to contact angle hysteresis and suppressed vaporization. The reduced evaporation has been attributed quantitatively to the existence of a constrained vapor-rich dome between the two droplets. However, a dynamic decrease in the droplet radius due to solvent removal marks a return to symmetry in terms of evaporation and contact angle. We have described the variation in evaporation flux using a universal correction factor. We have also demonstrated the existence of a critical separation distance beyond which the droplets in the, droplet pair do not affect each other. The results are crucial to a plethora of applications ranging from surface patterning to lab-on-a-chip devices.

Nanomechanical Mapping, Hierarchical Polymer Dynamics, and Miscibility in the Presence of Chain-End Grafted Nanoparticles

To improve the spatial distribution of nano particles in a polymeric host and to enhance the interfacial interaction with the host, the use of chain-end grafted nanoparticle has gained popularity in the field of polymeric nanocomposites. Besides changing the material properties of the host, these grafted nanoparticles strongly alter the dynamics of the polymer chain at both local and cooperative length scales (relaxations) by manipulating the enthalpic and entropic interactions. It is difficult to map the distribution of these chain-end grafted nanoparticles in the blend by conventional techniques, and herein, we attempted to characterize it by unique technique(s) like peak force quantitative nanomechanical mapping (PFQNM) through AFM (atomic force microscopy) imaging and dielectric relaxation spectroscopy (DRS). Such techniques, besides shedding light on the spatial distribution of the nanoparticles, also give critical information on the changing elasticity at smaller length scales and hierarchical polymer chain dynamics in the vicinity of the nanoparticles. The effect of one-dimensional rodlike multiwall carbon nanotubes (MWNTs), with the characteristic dimension of the order of the radius of gyration of the polymeric chain, on the phase miscibility and chain dynamics in a classical LCST mixture of polystyrene/ poly(vinyl methyl ether) (PS/PVME) was examined in detail using the above techniques. In order to tune the localization of the nanotubes, different molecular weights of PS (13, 31, and 46 kDa), synthesized using RAFT (reversible addition fragmentation chain transfer) polymerization, was grafted onto MWNTs in situ. The thermodynamic miscibility in the blends was assessed by low-amplitude isochronal temperature sweeps, the spatial distribution of MWNTs in the blends was evaluated by PFQNM, and the hierarchical polymer chain dynamics was studied by DRS. It was observed that the miscibility, concentration fluctuation, and cooperative relaxations of the PS/PVME blends are strongly governed by the spatial distribution of MWNTs in the blends. These findings should help guide theories and simulations of hierarchical chain dynamics in LCST mixtures containing rodlike nanoparticles.

A hybrid finite element formulation for flexible multibody dynamics

This work deals with the transient analysis of flexible multibody systems within a hybrid finite element framework. Hybrid finite elements are based on a two-field variational formulation in which the displacements and stresses are interpolated separately yielding very good coarse mesh accuracy. Most of the literature on flexible multibody systems uses beam-theory-based formulations. In contrast, the use of hybrid finite elements uses continuum-based elements, thus avoiding the problems associated with rotational degrees of freedom. In particular, any given three-dimensional constitutive relations can be directly used within the framework of this formulation. Since the coarse mesh accuracy as compared to a conventional displacement-based formulation is very high, the scheme is cost effective as well. A general formulation is developed for the constrained motion of a given point on a line manifold, using a total Lagrangian method. The multipoint constraint equations are implemented using Lagrange multipliers. Various kinds of joints such as cylindrical, prismatic, and screw joints are implemented within this general framework. Hinge joints such as spherical, universal, and revolute joints are obtained simply by using shared nodes between the bodies. In addition to joints, the formulation and implementation details for a DC motor actuator and for prescribed relative rotation are also presented. Several example problems illustrate the efficacy of the developed formulation.

Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone

Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm(-1) blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 1(1)n pi* (band I) and 1(1)pi pi* (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm(-1)), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to varying solvation dynamics. This will have implications for ultrafast processes associated with electron-transfer, charge transfer, and also the photophysical aspects of excited states. (C) 2016 AIP Publishing LLC.

Joint modeling of lithosphere and mantle dynamics: Evaluation of constraints from global tomography models

With the advances in technology, seismological theory, and data acquisition, a number of high-resolution seismic tomography models have been published. However, discrepancies between tomography models often arise from different theoretical treatments of seismic wave propagation, different inversion strategies, and different data sets. Using a fixed velocity-to-density scaling and a fixed radial viscosity profile, we compute global mantle flow models associated with the different tomography models and test the impact of these for explaining surface geophysical observations (geoid, dynamic topography, stress, and strain rates). We use the joint modeling of lithosphere and mantle dynamics approach of Ghosh and Holt (2012) to compute the full lithosphere stresses, except that we use HC for the mantle circulation model, which accounts for the primary flow-coupling features associated with density-driven mantle flow. Our results show that the seismic tomography models of S40RTS and SAW642AN provide a better match with surface observables on a global scale than other models tested. Both of these tomography models have important similarities, including upwellings located in Pacific, Eastern Africa, Iceland, and mid-ocean ridges in the Atlantic and Indian Ocean and downwelling flows mainly located beneath the Andes, the Middle East, and central and Southeast Asia.

Toward a High-Resolution Monitoring of Continental Surface Water Extent and Dynamics, at Global Scale: from GIEMS (Global Inundation Extent from Multi-Satellites) to SWOT (Surface Water Ocean Topography)

Up to now, high-resolution mapping of surface water extent from satellites has only been available for a few regions, over limited time periods. The extension of the temporal and spatial coverage was difficult, due to the limitation of the remote sensing technique e.g., the interaction of the radiation with vegetation or cloud for visible observations or the temporal sampling with the synthetic aperture radar (SAR)]. The advantages and the limitations of the various satellite techniques are reviewed. The need to have a global and consistent estimate of the water surfaces over long time periods triggered the development of a multi-satellite methodology to obtain consistent surface water all over the globe, regardless of the environments. The Global Inundation Extent from Multi-satellites (GIEMS) combines the complementary strengths of satellite observations from the visible to the microwave, to produce a low-resolution monthly dataset () of surface water extent and dynamics. Downscaling algorithms are now developed and applied to GIEMS, using high-spatial-resolution information from visible, near-infrared, and synthetic aperture radar (SAR) satellite images, or from digital elevation models. Preliminary products are available down to 500-m spatial resolution. This work bridges the gaps and prepares for the future NASA/CNES Surface Water Ocean Topography (SWOT) mission to be launched in 2020. SWOT will delineate surface water extent estimates and their water storage with an unprecedented spatial resolution and accuracy, thanks to a SAR in an interferometry mode. When available, the SWOT data will be adopted to downscale GIEMS, to produce a long time series of water surfaces at global scale, consistent with the SWOT observations.

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

Using a molecular model for octamethylcydotetrasiloxane (OMCTS), molecular dynamics simulations are carried out to probe the phase state of OMCTS confined between two mica surfaces in equilibrium With a reservoir. Molecular dynamics simulations are carried out for elevations ranging from 5 to 35 K above the melting point for the OMCTS model used in this study. The Helmholtz free energy is, computed for a specific confinement using the :two-phase thermodynamic (2PT) method. Analysis of the in-plane pair correlation functions did not reveal signatures of freezing even under an extreme confinement of two layers. OMCTS is found to orient with a wide distribution of orientations with respect to the mica surface, with a distinct preference for the surface parallel configuration in the contact layers. The self-intermediate scattering function is found to decay with increasing relaxation times as the surface separation is decreased, and the two-step relaxation in the scattering function, a signature of glassy dynamics, distinctly evolves as the temperature is lowered. However, even at 5 K above the melting point, we did not observe a freezing transition and the self-intermediate scattering functions relax within 200 ps for the seven-layered confined system. The self diffusivity and relaxation times obtained from the Kohlrausch-Williams-Watts stretched exponential fits to the late alpha-relaxation exhibit power law scalings with the packing fraction as predicted by mode coupling theory. A distinct discontinuity in the Helmholtz free energy, potential energy, and a sharp change in the local bond order parameter, Q(4), was observed at 230 K for a five-layered system upon cooling, indicative of a first-order transition. A freezing point depression of about 30 K was observed for this five-layered confined system, and at the lower temperatures, contact layers were found to be disordered with long-range order present only in the inner layers. These dynamical signatures indicate that confined OMCTS undergoes a slowdown akin to a fluid approaching a glass transition upon increasing confinement, and freezing under confinement would require substantial subcooling below the bulk melting point of OMCTS.

Modulation of Buckling Dynamics in Nanoparticle Laden Droplets Using External Heating

Dynamics of contact free (levitated) drying of nanofluid droplets is ubiquitous in many application domains ranging from spray drying to pharmaceutics. Controlling the final morphology (macro to micro scales) of the dried out sample poses some serious challenges. Evaporation of solvent and agglomeration of particles leads to porous shell formation in acoustically levitated nanosilica droplets. The capillary pressure due to evaporation across the menisci at the nanoscale pores causes buckling of the shell which leads to ring and bowl shaped final structures. Acoustics plays a crucial role in flattening of droplets which is a prerequisite for initiation of buckling in the shell: Introduction of mixed nanocolloids (sodium dodecyl sulfate + nanosilica) reduces evaporation rate, disrupts formation of porous shell, and enhances mechanical strength of the shell, all of which restricts the process of buckling. Although buckling is completely arrested in such surfactant added droplets, controlled external heating using laser enhances evaporation through the pores in the shell due to thermally induced structural changes and rearrangement of SDS aggregates which reinitializes buckling in such droplets, Furthermore, inclusion of anilinium hydrochloride into the nanoparticle laden droplets produces ions which adsorb and modify the morphology of sodium dodecyl sulfate crystals and reinitializes buckling in the shell (irrespective of external heating conditions). The kinetics of buckling is determined by the combined effect of morphology of the colloidal particles, particle/aggregate diffusion rate within the droplet, and the rate of evaporation of water. The buckling dynamics leads to cavity formation which grows subsequently to yield final structures with drastically different morphological features. The cavity growth is controlled by evaporation through the nanoscate pores and exhibits a universal trend irrespective of heating rate and nanoparticle type.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

Molecular dynamics simulation of the role of dislocations in microcrack healing

The molecular dynamics method is used to simulate microcrack healing during heating or/and under compressive stress. A centre microcrack in Cu crystal would be sealed under compressive stress or by heating. The role of compressive stress and heating in crack healing was additive. During microcrack healing, dislocation generation and motion occurred. When there were pre-existing dislocations around the microcrack, the critical temperature or compressive stress necessary for microcrack healing would decrease, and, the higher the number of dislocations, the lower the critical temperature or compressive stress. The critical temperature necessary for microcrack healing depended upon the orientation of the crack plane. For example, the critical temperature for the crack along the (001) plane was the lowest, i.e. 770K.