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Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.
Automated deduction in higher-order program calculi, where properties of transformation rules are demanded, or confluence or other equational properties are requested, can often be done by syntactically computing overlaps (critical pairs) of reduction rules and transformation rules. Since higher-order calculi have alpha-equivalence as fundamental equivalence, the reasoning procedure must deal with it. We define ASD1-unification problems, which are higher-order equational unification problems employing variables for atoms, expressions and contexts, with additional distinct-variable constraints, and which have to be solved w.r.t. alpha-equivalence. Our proposal is to extend nominal unification to solve these unification problems. We succeeded in constructing the nominal unification algorithm NomUnifyASC. We show that NomUnifyASC is sound and complete for these problem class, and outputs a set of unifiers with constraints in nondeterministic polynomial time if the final constraints are satisfiable. We also show that solvability of the output constraints can be decided in NEXPTIME, and for a fixed number of context-variables in NP time. For terms without context-variables and atom-variables, NomUnifyASC runs in polynomial time, is unitary, and extends the classical problem by permitting distinct-variable constraints.
1998 ACM Subject Classification F.4.1 Mathematical Logic