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According to the statistical interpretation of quantum theory, quantum computers form a distinguished class of probabilistic machines (PMs) by encoding n qubits in 2n pbits (random binary variables). This raises the possibility of a…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
The Boltzmann Machine (BM) is a neural network composed of stochastically firing neurons that can learn complex probability distributions by adapting the synaptic interactions between the neurons. BMs represent a very generic class of…
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of…
Probabilistic Quantum Memory (PQM) is a data structure that computes the distance from a binary input to all binary patterns stored in superposition on the memory. This data structure allows the development of heuristics to speed up…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
Artificial neural networks have been proposed as potential algorithms that could benefit from being implemented and run on quantum computers. In particular, they hold promise to greatly enhance Artificial Intelligence tasks, such as image…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…
Mathematical Program Networks (MPNs) are introduced in this work. An MPN is a collection of interdependent Mathematical Programs (MPs) which are to be solved simultaneously, while respecting the connectivity pattern of the network defining…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…
Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…
Digital memcomputing machines (DMMs) are a class of computational machines designed to solve combinatorial optimization problems. A practical realization of DMMs can be accomplished via electrical circuits of highly non-linear,…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…
In this study, a distinctive feature of quantum computation (QC) is characterized. To this end, a seemingly-powerful classical computing model, called "stochastic ensemble machine (SEnM)," is considered. The SEnM runs with an ensemble…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…