Freedom of additional signals on genes: on the combination of DNA mechanics, genetics and translation speed

DNA carries various forms of information. Out of these forms of information the most well-known is classical genetic information. Throughout this dissertation we discuss what is often referred to as the second layer of information on DNA: DNA mechanics. A sequence consisting of only A’s and T’s will bend differently from a sequence of G’s and C’s. An important consequence of this mechanical layer of information is the positioning of nucleosomes. Nucleosomes consist of 147 base pairs of DNA wrapped around a protein core, like a string around a spool. By either allowing or restricting access to a binding site, a nucleosome may serve as an on/off switch, of which the location is extremely important. A third layer of information on DNA is translation speed. Translation speed refers to the rate at which a protein is created, and it depends on the codons used in a genetic sequence. The research in this thesis investigates how these layers of information are multiplexed. It uses multiple novel approaches, one of them being the use of weighted graphs consisting of all possible DNA sequences to find the very best and very worst nucleosome-attracting sequences. Theoretical Physic

Larger Corner-Free Sets from Combinatorial Degenerations

There is a large and important collection of Ramsey-type combinatorial problems, closely related to central problems in complexity theory, that can be formulated in terms of the asymptotic growth of the size of the maximum independent sets in powers of a fixed small (directed or undirected) hypergraph, also called the Shannon capacity. An important instance of this is the corner problem studied in the context of multiparty communication complexity in the Number On the Forehead (NOF) model. Versions of this problem and the NOF connection have seen much interest (and progress) in recent works of Linial, Pitassi and Shraibman (ITCS 2019) and Linial and Shraibman (CCC 2021). We introduce and study a general algebraic method for lower bounding the Shannon capacity of directed hypergraphs via combinatorial degenerations, a combinatorial kind of "approximation" of subgraphs that originates from the study of matrix multiplication in algebraic complexity theory (and which play an important role there) but which we use in a novel way. Using the combinatorial degeneration method, we make progress on the corner problem by explicitly constructing a corner-free subset in $F_2^n \times F_2^n$ of size $\Omega(3.39^n/poly(n))$, which improves the previous lower bound $\Omega(2.82^n)$ of Linial, Pitassi and Shraibman (ITCS 2019) and which gets us closer to the best upper bound $4^{n - o(n)}$. Our new construction of corner-free sets implies an improved NOF protocol for the Eval problem. In the Eval problem over a group $G$, three players need to determine whether their inputs $x_1, x_2, x_3 \in G$ sum to zero. We find that the NOF communication complexity of the Eval problem over $F_2^n$ is at most $0.24n + O(\log n)$, which improves the previous upper bound $0.5n + O(\log n)$.Comment: A short version of this paper will appear in the proceedings of ITCS 2022. This paper improves results that appeared in arxiv:2104.01130v

The role of transcript regions and amino acid choice in nucleosome positioning

Theoretical Physic

Discreteness of asymptotic tensor ranks

Tensor parameters that are amortized or regularized over large tensor powers, often called "asymptotic" tensor parameters, play a central role in several areas including algebraic complexity theory (constructing fast matrix multiplication algorithms), quantum information (entanglement cost and distillable entanglement), and additive combinatorics (bounds on cap sets, sunflower-free sets, etc.). Examples are the asymptotic tensor rank, asymptotic slice rank and asymptotic subrank. Recent works (Costa-Dalai, Blatter-Draisma-Rupniewski, Christandl-Gesmundo-Zuiddam) have investigated notions of discreteness (no accumulation points) or "gaps" in the values of such tensor parameters. We prove a general discreteness theorem for asymptotic tensor parameters of order-three tensors and use this to prove that (1) over any finite field (and in fact any finite set of coefficients in any field), the asymptotic subrank and the asymptotic slice rank have no accumulation points, and (2) over the complex numbers, the asymptotic slice rank has no accumulation points. Central to our approach are two new general lower bounds on the asymptotic subrank of tensors, which measures how much a tensor can be diagonalized. The first lower bound says that the asymptotic subrank of any concise three-tensor is at least the cube-root of the smallest dimension. The second lower bound says that any concise three-tensor that is "narrow enough" (has one dimension much smaller than the other two) has maximal asymptotic subrank. Our proofs rely on new lower bounds on the maximum rank in matrix subspaces that are obtained by slicing a three-tensor in the three different directions. We prove that for any concise tensor, the product of any two such maximum ranks must be large, and as a consequence there are always two distinct directions with large max-rank