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Anton Zadorin

Publications and source records attributed to Anton Zadorin.

3 recordsLinked to original sources

Dynamical perturbation theory for eigenvalue problems

Many problems in physics, chemistry and other fields are perturbative in nature, i.e. differ only slightly from related problems with known solutions. Prominent among these is the eigenvalue perturbation problem, wherein one seeks the eigenvectors and eigenvalues of a matrix with small off-diagonal elements. Here we introduce a novel iterative algorithm to compute these eigenpairs based on fixed-point iteration for an algebraic equation in complex projective space. We show from explicit and numerical examples that our algorithm outperforms the usual Rayleigh-Schrödinger expansion on three counts. First, since it is not defined as a power series, its domain of convergence is not a priori confined to a disk in the complex plane; we find that it indeed usually extends beyond the standard perturbative radius of convergence. Second, it converges at a faster rate than the Rayleigh-Schrödinger expansion, i.e. fewer iterations are required to reach a given precision. Third, the (time- and space-) algorithmic complexity of each iteration does not increase with the order of the approximation, allowing for higher precision computations. Because this complexity is merely that of matrix multiplication, our dynamical scheme also scales better with the size of the matrix than general-purpose eigenvalue routines such as the shifted QR or divide-and-conquer algorithms. Whether they are dense, sparse, symmetric or unsymmetric, we confirm that dynamical diagonalization quickly outpaces LAPACK drivers as the size of matrices grows; for the computation of just the dominant eigenvector, our method converges order of magnitudes faster than the Arnoldi algorithm implemented in ARPACK.

math-ph↗

Synthesis and materialization of a reaction-diffusion French flag pattern

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. Firstly, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically-distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Secondly, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental program.

nlin.PS↗

Quantifying the performance of high-throughput directed evolution protocols

Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants. We introduce here a new metric named the Selection Quality Index (SQI), which can be computed from a simple mock experiment with a known initial fraction of active variants. As opposed to previous approaches, our index integrates the random co-encapsulation of entities in compartments and comes with a straightforward experimental interpretation. We further show how this new metric can be used to extract general trends of protocol efficiency, or reveal hidden mechanisms such as a counterintuitive form of beneficial poisoning in the Compartmentalized Self-Replication protocol.

q-bio.PE↗