A divide and conquer real space finite-element Hartree-Fock method.

Since the seminal contribution of Roothaan, quantum chemistry methods are traditionally expressed using finite basis sets comprised of smooth and continuous functions (atom-centered Gaussians) to describe the electronic degrees of freedom. Although this approach proved quite powerful, it is not well suited for large basis sets because of linear dependence problems and ill conditioning of the required matrices. The finite element method (FEM), on the other hand, is a powerful numerical method whose convergence is also guaranteed by variational principles and can be achieved systematically by increasing the number of degrees of freedom and/or the polynomial order of the shape functions. Here we apply the real-space FEM to Hartree-Fock calculations in three dimensions. The method produces sparse, banded Hermitian matrices while allowing for variable spatial resolution. This local-basis approach to electronic structure theory allows for systematic convergence and promises to provide an accurate and efficient way toward the full ab initio analysis of materials at larger scales. We introduce a new acceleration technique for evaluating the exchange contribution within FEM and explore the accuracy and robustness of the method for some selected test atoms and molecules. Furthermore, we applied a divide-and-conquer (DC) method to the finite-element Hartree-Fock ab initio electronic-structure calculations in three dimensions. This DC approach leads to facile parallelization and should enable reduced scaling for large systems.

Stamp collapse in soft lithography.

We have studied the so-called roof collapse in soft lithography. Roof collapse is due to the adhesion between the PDMS stamp and substrate, and it may affect the quality of soft lithography. Our analysis accounts for the interactions of multiple punches and the effect of elastic mismatch between the PDMS stamp and substrate. A scaling law among the stamp modulus, punch height and spacing, and work of adhesion between the stamp and substrate is established. Such a scaling law leads to a simple criterion against the unwanted roof collapse. The present study agrees well with the experimental data.

Production of defective virus by terminally differentiated myotubes infected with Rous sarcoma virus.

The generally accepted concept that the replication of Rous sarcoma virus (RSV) is dependent on host cell DNA synthesis was reexamined. As the host we used terminally differentiated myotubes (MT), in which no cellular DNA synthesis is observed. As an extension of our previous study which indicated that RSV-infected MT produce various virus components, we examined viral particles produced by infected MT. Electron microscopy showed presence of viral particles released from infected MT. Immunoprecipitation analysis revealed that these particles contained an equal amount of the gag but a decreased amount of the env proteins as compared with the particles from infected chicken embryo fibroblasts (CEF). Consequently, viral particles from infected MT had an infectivity only 6% of that of particles from infected CEF cells. In a parallel experiment, we microinjected molecularly cloned RSV DNA into MT. In contrast to the infection mediated by viral particles, both MT and CEF cells produced the same amount of infectious particles when microinjected with viral DNA. We conclude that RSV replicates in the complete absence of host DNA synthesis, though infectivity of the progeny virus depends on the initial condition of the infection.

Infection of terminally differentiated myotubes with Rous sarcoma virus: reduced synthesis of env and v-src proteins.

We studied Rous sarcoma virus (RSV) protein synthesis in RSV-infected, terminally differentiated chicken myotubes ('late-infected' myotubes), in which no viral DNA integration takes place but all three viral mRNAs (38S, 28S and 21S) are transcribed normally. With the use of specific anti-RSV protein antisera, we found that only the viral gag and pol proteins were synthesized at levels similar to those synthesized in RSV-transformed fibroblasts; the synthesis of env and v-src proteins was significantly reduced in these infected myotubes. We concluded that the viral RNA transcribed from the unintegrated RSV DNA was functional but that genes at the 3' end of the RSV genome were translated at a lower level. By contrast, when mononucleated replicating chicken myoblasts were infected with a mutant (tsNY68) carrying a temperature-sensitive v-src gene and maintained at the non-permissive temperature for this gene, they developed into myotubes with viral DNA integrated in their chromosomal DNA. These 'early-infected' myotubes expressed all four viral genes (gag, pol, env and v-src) at a level similar to that in infected fibroblasts. This result ruled out the possible presence of specific factor(s) in myotubes that preferentially inhibit the 3' genes of RSV, and suggested other translational control(s) of viral gene expression in late-infected myotubes.