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Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…
Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction is required to improve assembly yield beyond equilibrium limits,…
Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select'…
Quantum Entanglement is a fundamentally important resource in Quantum Information Science; however, generating it in practice is plagued by noise and decoherence, limiting its utility. Entanglement distillation and forward error correction…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…
Directed evolution is an iterative laboratory process of designing proteins with improved function by iteratively synthesizing new protein variants and evaluating their desired property with expensive and time-consuming biochemical…
The min-cost matching problem suffers from being very sensitive to small changes of the input. Even in a simple setting, e.g., when the costs come from the metric on the line, adding two nodes to the input might change the optimal solution…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
Geochemical data provide key information on the timing of accretion and on the prevailing physical conditions during core/mantle differentiation. However, their interpretation depends critically on the efficiency of metal/silicate chemical…
In the design of stellarators, energetic particle confinement is a critical point of concern which remains challenging to study from a numerical point of view. Standard Monte Carlo analyses are highly expensive because a large number of…
High-level synthesis, source-to-source compilers, and various Design Space Exploration techniques for pragma insertion have significantly improved the Quality of Results of generated designs. These tools offer benefits such as reduced…
In modular robotics, modules can be reconfigured to change the morphology of the robot, making it able to adapt for specific tasks. However, optimizing both the body and control is a difficult challenge due to the intricate relationship…
Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction…
Controlled feature selection aims to discover the features a response depends on while limiting the false discovery rate (FDR) to a predefined level. Recently, multiple deep-learning-based methods have been proposed to perform controlled…
Readout of superconducting qubits faces a trade-off between measurement speed and unwanted back-action on the qubit caused by the readout drive, such as $T_1$ degradation and leakage out of the computational subspace. The readout is…
Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…