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Models for complex systems are often built with more parameters than can be uniquely identified by available data. Because of the variety of causes, identifying a lack of parameter identifiability typically requires mathematical…
Structure-based molecular ML (SBML) models can be highly sensitive to input geometries and give predictions with large variance. We present an approach to mitigate the challenge of selecting conformations for such models by generating…
Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges.…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
Rapid determination of molecular structures can greatly accelerate workflows across many chemical disciplines. However, elucidating structure using only one-dimensional (1D) NMR spectra, the most readily accessible data, remains an…
Understanding material surfaces and interfaces is vital in applications like catalysis or electronics. By combining energies from electronic structure with statistical mechanics, ab initio simulations can in principle predict the structure…
Materials with bespoke properties have long been identified by computational searches, and their experimental realisation is now coming within reach through autonomous laboratories. Scattering experiments are central to verifying the atomic…
The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
This work focuses on effectively generating diverse solutions for satisfiability modulo theories (SMT) formulas, targeting the theories of bit-vectors, arrays, and uninterpreted functions, which is a critical task in software and hardware…
We present a new use of Answer Set Programming (ASP) to discover the molecular structure of chemical samples based on the relative abundance of elements and structural fragments, as measured in mass spectrometry. To constrain the…
The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan…
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…
Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then…
In this work, methods are presented to automatically generate a fully atomistic LAMMPS models of arbitrary linear multiblock polyurethane copolymers. The routine detailed here receives as parameters the number of repeat units per hard…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
Simulated Moving Bed (SMB) chromatography is a well-known technique for the resolution of several high-value-added compounds. Parameters identification and model topology definition are arduous when one is dealing with complex systems such…
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…