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In a Merlin-Arthur proof system, the proof verifier (Arthur) accepts valid proofs (from Merlin) with probability 1, and rejects invalid proofs with probability arbitrarily close to 1. The running time of such a system is defined to be the length of Merlin’s proof plus the running time of Arthur. We provide new Merlin-Arthur proof systems for some key problems in fine-grained complexity. In several cases our proof systems have optimal running time. Our main results include: - Certifying that a list of n integers has no 3-SUM solution can be done in Merlin-Arthur time Õ(n). Previously, Carmosino et al. [ITCS 2016] showed that the problem has a nondeterministic algorithm running in Õ(n^{1.5}) time (that is, there is a proof system with proofs of length Õ(n^{1.5}) and a deterministic verifier running in Õ(n^{1.5}) time). - Counting the number of k-cliques with total edge weight equal to zero in an n-node graph can be done in Merlin-Arthur time Õ(n^{⌈ k/2⌉}) (where k ≥ 3). For odd k, this bound can be further improved for sparse graphs: for example, counting the number of zero-weight triangles in an m-edge graph can be done in Merlin-Arthur time Õ(m). Previous Merlin-Arthur protocols by Williams [CCC'16] and Björklund and Kaski [PODC'16] could only count k-cliques in unweighted graphs, and had worse running times for small k. - Computing the All-Pairs Shortest Distances matrix for an n-node graph can be done in Merlin-Arthur time Õ(n²). Note this is optimal, as the matrix can have Ω(n²) nonzero entries in general. Previously, Carmosino et al. [ITCS 2016] showed that this problem has an Õ(n^{2.94}) nondeterministic time algorithm. - Certifying that an n-variable k-CNF is unsatisfiable can be done in Merlin-Arthur time 2^{n/2 - n/O(k)}. We also observe an algebrization barrier for the previous 2^{n/2}⋅ poly(n)-time Merlin-Arthur protocol of R. Williams [CCC'16] for #SAT: in particular, his protocol algebrizes, and we observe there is no algebrizing protocol for k-UNSAT running in 2^{n/2}/n^{ω(1)} time. Therefore we have to exploit non-algebrizing properties to obtain our new protocol. - Certifying a Quantified Boolean Formula is true can be done in Merlin-Arthur time 2^{4n/5}⋅ poly(n). Previously, the only nontrivial result known along these lines was an Arthur-Merlin-Arthur protocol (where Merlin’s proof depends on some of Arthur’s coins) running in 2^{2n/3}⋅poly(n) time. Due to the centrality of these problems in fine-grained complexity, our results have consequences for many other problems of interest. For example, our work implies that certifying there is no Subset Sum solution to n integers can be done in Merlin-Arthur time 2^{n/3}⋅poly(n), improving on the previous best protocol by Nederlof [IPL 2017] which took 2^{0.49991n}⋅poly(n) time.