The surging interest in manipulating the polarization of piezo/ferroelectric materials by means of light has driven an increasing number of studies toward their light-polarization interaction. One way to investigate such interaction is by performing piezoresponse force microscopy (PFM) while/after the sample is exposed to light illumination. However, caution must be exercised when analyzing and interpreting the data, as demonstrated in this paper, because sizeable photo-response observed in the PFM amplitude image of the sample is shown to be caused by the electrostatic interaction between the photo-induced surface charge and tip. Through photo-assisted Kelvin probe force microscopy (KPFM), positive surface potential is found to be developed near the sample's surface under 405 nm light illumination, whose effects on the measured PFM signal is revealed by the comparative studies on its amplitude curves that are obtained using PFM spectroscopy mode with/without illumination. This work exemplifies the need for complementary use of KPFM, PFM imaging mode, and PFM spectroscopy mode in order to distinguish real behavior from artifacts.

The phase behaviour of aqueous suspensions of NAu1 nontronite was studied on size-selected particles by combining osmotic pressure measurements, visual observations under polarized light, rheological experiments and Small Angle X-ray Scattering (SAXS). NAu1 suspensions display a liquid crystalline behaviour as they exhibit a Isotropic/Nematic (I/N) transition that occurs before the sol/gel transition for ionic strengths below 10–3 M/L. This I/N transition shifts towards lower volume fractions for increasing particle anisotropy and its position in the phase diagram agrees well with the theoretical predictions for platelets. SAXS measurements reveal the presence of characteristic interparticular distances in the isotropic, nematic and gel phases. In the gel phase a local lamellar order is observed which shows that the “house of cards” model is not appropriate for describing the gel structure in swelling clay materials at low ionic strength. Furthermore, by combining results from osmotic pressure measurements and X-ray scattering, it appears that the pressure of the system can be well described using a simple Poisson-Boltzmann treatment based on the repulsion between charged infinite parallel planes. In terms of rheological properties, even if the thermodynamical status of the sol/gel transition remains partially unclear, the yield stress and elasticity of the gels can be easily renormalized for all particle sizes on the basis of the volume of the particles. Furthermore, rheological modelling of the flow curves shows that for all the particles an approach based on excluded volume effects captures most features of nontronite suspensions.

Laboratory experiments were conducted to determine the effects of application factors and standing Triticum aestivum stubble on herbicide spray deposition and efficacy in a simulated no-till environment. Spray deposition on weeds was reduced in the presence of stubble, and deposition losses on Amaranthus hybridus were greater than those on Setaria faberi. Spray penetration through stubble was significantly enhanced with electrostatic charging of a fine hydraulic spray. The combination of 45 kV electrostatic charge and 50 cm nozzle spacing produced maximum spray deposition on weeds and resulted in a 96% and 345% increase in deposition on A. hybridus and S. faberi, respectively, compared to the uncharged controls. Deposit reduction from standing stubble was greater at travel speeds of 16 km h−1 (36 to 52%) than 8 km h−1 (9 to 38%). On a dry weight and plant density basis, weeds retained more spray than was retained by stubble, yet stubble, at average densities, was capable of capturing 9 to 12% of total applied spray dose per unit area. Bounce studies of individual droplets of water or imazethapyr plus adjuvant mixture demonstrated that T. aestivum straw had a general affinity for all spray droplets, exhibiting no rebound even for 800-µm water droplets. Setaria faberi foliage exhibited poor retention of droplets: both 350- and 800-µm water droplets as well as 800-µm droplets of imazethapyr plus adjuvant mixture rebounded. Only 350-µm herbicide mixture droplets were retained by S. faberi. Amaranthus hybridus retained all droplets. In broadcast spraying, British Crop Protection Council “Medium” quality sprays were poorly retained by S. faberi compared to “Fine” sprays, whereas A. hybridus retained both sprays equally well. However, imazethapyr spray deposits resulting from coarser sprays were more efficacious on S. faberi than fine spray deposits, a difference that was not observed for A. hybridus.

Even though there are various fast methods and preconditioning techniques available for the simulation of Poisson problems, little work has been done for solving Poisson's equation by using the Helmholtz decomposition scheme. To bridge this issue, we propose a novel efficient algorithm to solve Poisson's equation in irregular two dimensional domains for electrostatics through a quasi-Helmholtz decomposition technique—the loop-tree basis decomposition. It can handle Dirichlet, Neumann or mixed boundary problems in which the filling media can be homogeneous or inhomogeneous. A novel point of this method is to first find the electric flux efficiently by applying the loop-tree basis functions. Subsequently, the potential is obtained by finding the inverse of the gradient operator. Furthermore, treatments for both Dirichlet and Neumann boundary conditions are addressed. Finally, the validation and efficiency are illustrated by several numerical examples. Through these simulations, it is observed that the computational complexity of our proposed method almost scales as , where N is the triangle patch number of meshes. Consequently, this new algorithm is a feasible fast Poisson solver.

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the nodepatch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt-bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism.

Cell motility is an integral part of a diverse set of biological processes. The quest formathematical models of cell motility has prompted the development of automated approachesfor gathering quantitative data on cell morphology, and the distribution of molecularplayers involved in cell motility. Here we review recent approaches for quantifying cellmotility, including automated cell segmentation and tracking. Secondly, we present our ownnovel method for tracking cell boundaries of moving cells, the Electrostatic ContourMigration Method (ECMM), as an alternative to the generally accepted level set method(LSM). ECMM smoothly tracks regions of the cell boundary over time to compute localmembrane displacements using the simple underlying concept of electrostatics. It offerssubstantial speed increases and reduced computational overheads in comparison to the LSM.We conclude with general considerations regarding boundary tracking in the context ofmathematical modelling.

Pure rat brain tubulin is readily palmitoylated in vitro using [3H]palmitoyl CoA but no added enzymes. A maximum of approximately six palmitic acids are added per dimer in 2–3 h at 36–37 °C under native conditions. Both α and β tubulin are labeled, and 63–73% of the label was hydroxylamine-labile, presumed thioesters. Labeling increases with increasing pH and temperature, and with low concentrations of guanidine HCl or KCl (but not with urea) to a maximum of ∼13 palmitates/dimer. High SDS and guanidine HCl concentrations are inhibitory. At no time could all 20 cysteine residues of the dimer be palmitoylated. Polymerization to microtubules, or use of tubulin S, markedly decreases the accessibility of the palmitoylation sites. Palmitoylation increases the electrophoretic mobility of a portion of α tubulin toward the β band. Palmitoylated tubulin binds a colchicine analogue normally, but during three warm/cold polymerization/depolymerization cycles there is a progressive loss of palmitoylated tubulin, indicating decreased polymerization competence. We postulate that local electrostatic factors are major regulators of reactivity of tubulin cysteine residues toward palmitoyl CoA, and that the negative charges surrounding a number of the cysteines are sensitive to negative charges on palmitoyl CoA.

The human Theta class glutathione transferase GSTT2-2 has a novel sulfatase activity that is not dependent on the presence of a conserved hydrogen bond donor in the active site. Initial homology modeling and the crystallographic studies have identified three conserved Arg residues that contribute to the formation of (Arg107 and Arg239), and entry to (Arg242), a sulfate binding pocket. These residues have been individually mutated to Ala to investigate their potential role in substrate binding and catalysis. The mutation of Arg107 had a significant detrimental effect on the sulfatase reaction, while the Arg242 mutation caused only a small reduction in sulfatase activity. Surprisingly, the Arg239 had an increased activity resulting from a reduction in stability. Thus, Arg239 appears to play a role in maintaining the architecture of the active site. Electrostatic calculations performed on the wild-type and mutant forms of the enzyme are in good agreement with the experimental results. These findings, along with docking studies, suggest that prior to conjugation, the location of 1-menaphthyl sulfate, a model substrate for the sulfatase reaction, is approximately midway between the position ultimately occupied by the naphthalene ring of 1-menaphthylglutathione and the free sulfate. It is further proposed that the Arg residues in and around the sulfate binding pocket have a role in electrostatic substrate recognition.