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Abstract We introduce the kernel-elastic autoencoder (KAE), a self-supervised generative model based on the transformer architecture with enhanced performance for molecular design. KAE employs two innovative loss functions: modified maximum mean discrepancy (m-MMD) and weighted reconstruction (LWCEL). The m-MMD loss has significantly improved the generative performance of KAE when compared to using the traditional Kullback–Leibler loss of VAE, or standard maximum mean discrepancy. Including the weighted reconstruction loss LWCEL, KAE achieves valid generation and accurate reconstruction at the same time, allowing for generative behavior that is intermediate between VAE and autoencoder not available in existing generative approaches. Further advancements in KAE include its integration with conditional generation, setting a new state-of-the-art benchmark in constrained optimizations. Moreover, KAE has demonstrated its capability to generate molecules with favorable binding affinities in docking applications, as evidenced by AutoDock Vina and Glide scores, outperforming all existing candidates from the training dataset. Beyond molecular design, KAE holds promise to solve problems by generation across a broad spectrum of applications. 

Abstract We introduce a family of variational quantum algorithms, which we coin as quantum iterative power algorithms (QIPAs), and demonstrate their capabilities as applied to global-optimization numerical experiments. Specifically, we demonstrate the QIPA based on a double exponential oracle as applied to ground state optimization of theH₂molecule, search for the transmon qubit ground-state, and biprime factorization. Our results indicate that QIPA outperforms quantum imaginary time evolution (QITE) and requires a polynomial number of queries to reach convergence even with exponentially small overlap between an initial quantum state and the final desired quantum state, under some circumstances. We analytically show that there exists an exponential amplitude amplification at every step of the variational quantum algorithm, provided the initial wavefunction has non-vanishing probability with the desired state and that the unique maximum of the oracle is given by ${\lambda }_1>0$, while all other values are given by the same value $0<{\lambda }_2<{\lambda }_1$(hereλcan be taken as eigenvalues of the problem Hamiltonian). The generality of the global-optimization method presented here invites further application to other problems that currently have not been explored with QITE-based near-term quantum computing algorithms. Such approaches could facilitate identification of reaction pathways and transition states in chemical physics, as well as optimization in a broad range of machine learning applications. The method also provides a general framework for adaptation of a class of classical optimization algorithms to quantum computers to further broaden the range of algorithms amenable to implementation on current noisy intermediate-scale quantum computers. 

The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.