Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation

Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus‐like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid‐19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre‐existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer‐designed VLP not only to monomers (SARS‐CoV‐2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag‐mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.     

The inverse inertia problem for graphs: Cut vertices, trees, and a counterexample

Let G be an undirected graph on n vertices and let S(G) be the set of all real symmetric n×n matrices whose nonzero off-diagonal entries occur in exactly the positions corresponding to the edges of G. The inverse inertia problem for G asks which inertias can be attained by a matrix in S(G). We give a complete answer to this question for trees in terms of a new family of graph parameters, the maximal disconnection numbers of a graph. We also give a formula for the inertia set of a graph with a cut vertex in terms of inertia sets of proper subgraphs. Finally, we give an example of a graph that is not inertia-balanced, which settles an open problem from the October 2006 AIM Workshop on Spectra of Families of Matrices described by Graphs, Digraphs and Sign Patterns. We also determine some restrictions on the inertia set of any graph.     

Parametric approximation of isotropic and anisotropic elastic flow for closed and open curves

Deckelnick and Dziuk (Math. Comput. 78(266):645–671, 2009) proved a stability bound for a continuous-in-time semidiscrete parametric finite element approximation of the elastic flow of closed curves in \mathbbR^d, d 3 2{\mathbb{R}^d, d\geq2} . We extend these ideas in considering an alternative finite element approximation of the same flow that retains some of the features of the formulations in Barrett et al. (J Comput Phys 222(1): 441–462, 2007; SIAM J Sci Comput 31(1):225–253, 2008; IMA J Numer Anal 30(1):4–60, 2010), in particular an equidistribution mesh property. For this new approximation, we obtain also a stability bound for a continuous-in-time semidiscrete scheme. Apart from the isotropic situation, we also consider the case of an anisotropic elastic energy. In addition to the evolution of closed curves, we also consider the isotropic and anisotropic elastic flow of a single open curve in the plane and in higher codimension that satisfies various boundary conditions.     

Computing inertia sets using atoms

We consider the problem of computing inertia sets for graphs. By using tools for combining the inertia sets of smaller graphs we can reduce this problem to understanding the inertia sets for three-connected graphs that are not joins. We term such graphs atoms and give the inertia sets for all atoms on at most seven vertices. This can be used to compute the inertia sets for all graphs on at most seven vertices.     

An improved error bound for a finite element approximation of a model for phase separation of a multi-component alloy

Using the approach of Rulla (1996 SIAM J. Numer. Anal. 33, 68-87)for analysing the time discretization error and assuming moreregularity on the initial data, we improve on the error boundderived by Barrett and Blowey (1996 IMA J. Numer. Anal. 16,257-287) for a fully practical piecewise linear finite elementapproximation with a backward Euler time discretization of amodel for phase separation of a multi-component alloy.     

A weight-function approach for determining watershed initial conditions for combustion waves

In many generic combustion models, one finds that a combustionwave will develop with a specific wave speed. However, thereare possible initial temperature profiles which do not evolveinto such waves, but rather die out to the ambient temperature.There can exist, in some models, a clear distinction betweenthose initial conditions that do evolve into combustion wavesand those that do not; this is sometimes referred to as thewatershed initial condition. When fuel consumption is consideredto be negligible, analytical methods can be used to obtain theexact watershed. In this paper, we consider the problem of determiningpseudo-watersheds and ascertaining the relationship betweenthese pseudo-watersheds and the exact watersheds. In the processa novel weight-function approach for infinite spatial domainsis developed.     

Even-aged restrictions with sub-graph adjacency

Restrictions on the size and proximity of clearcuts have led to the development of a variety of exact and heuristic methods to optimize the net present value of timber harvests, subject to adjacency constraints. Most treat harvest units as pre-defined, and impose adjacency constraints on any two units sharing a common border. By using graph theory notation to define sub-graph adjacency constraints, opening size can be considered variable, which may be more appropriate for landscape-level planning. A small example data set is used in this paper to demonstrate the difference between the two types of adjacency constraints for both integer programming and heuristic solution methods.     

A variational formulation of anisotropic geometric evolution equations in higher dimensions

We present a novel variational formulation of fully anisotropic motion by surface diffusion and mean curvature flow in , d ≥ 2. This new formulation leads to an unconditionally stable, fully discrete, parametric finite element approximation in the case d = 2 or 3. The resulting scheme has very good properties with respect to the distribution of mesh points and, if applicable, volume conservation. This is demonstrated by several numerical experiments for d = 3, including regularized crystalline mean curvature flow and regularized crystalline surface diffusion.     

The finite element approximation of a coupled reaction-diffusion problem with non-Lipschitz nonlinearities

Summary. A coupled semilinear elliptic problem modelling an irreversible, isothermal chemical reaction is introduced, and discretised using the usual piecewise linear Galerkin finite element approximation. An interesting feature of the problem is that a reaction order of less than one gives rise to a "dead core" region. Initially, one reactant is assumed to be acting as a catalyst and is kept constant. It is shown that error bounds previously obtained for a scheme involving numerical integration can be improved upon by considering a quadratic regularisation of the nonlinear term. This technique is then applied to the full coupled problem, and optimal and error bounds are proved in the absence of quadrature. For a scheme involving numerical integration, bounds similar to those obtained for the catalyst problem are shown to hold. Received May 25, 1993 / Revised version received July 5, 1994