Related papers: Predicting 3D RNA Folding Patterns via Quadratic B…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…
Combinatorial optimization problems are typically formulated using Quadratic Unconstrained Binary Optimization (QUBO), where constraints are enforced through penalty terms that introduce auxiliary variables and rapidly increase Hamiltonian…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware…
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate…
The broad applicability of Quadratic Unconstrained Binary Optimization (QUBO) constitutes a general-purpose modeling framework for combinatorial optimization problems and are a required format for gate array and quantum annealing computers.…
In recent years, there has been significant research interest in solving Quadratic Unconstrained Binary Optimisation (QUBO) problems. Physics-inspired optimisation algorithms have been proposed for deriving optimal or sub-optimal solutions…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
The Quadratic Unconstrained Binary Optimization (QUBO) modeling and solution framework is a requirement for quantum and digital annealers. However optimality for QUBO problems of any practical size is extremely difficult to achieve. In…
Quantum and quantum-inspired optimisation algorithms are designed to solve problems represented in binary, quadratic and unconstrained form. Combinatorial optimisation problems are therefore often formulated as Quadratic Unconstrained…
Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
The inverse design of RNA three-dimensional (3D) structures is crucial for engineering functional RNAs in synthetic biology and therapeutics. While recent deep learning approaches have advanced this field, they are typically optimized and…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…
In this paper, we develop a way to encode several NP-Complete problems in Abstract Argumentation to Quadratic Unconstrained Binary Optimization (QUBO) problems. In this form, a solution for a QUBO problem involves minimizing a quadratic…
The RNA inverse folding problem aims to identify nucleotide sequences that preferentially adopt a given target secondary structure. While various heuristic and machine learning-based approaches have been proposed, many require a large…
Quadratic unconstrained binary optimization (QUBO) has become the standard format for optimization using quantum computers, i.e., for both the quantum approximate optimization algorithm (QAOA) and quantum annealing (QA). We present a…