Related papers: Sequence Engineering of Copolymers using Evolution…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…
Molecular self-assembly plays a very important role in various aspects of technology as well as in biological systems. Governed by the covalent, hydrogen or van der Waals interactions - self-assembly of alike molecules results in a large…
Recent development in computer processing power leads to new paradigms of how problems in many-body physics and especially polymer physics can be addressed. GPU parallel processors can be employed to generate millions of independent…
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property using both artificial neural networks and mixed integer linear programming. In this paper, we design a…
Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to…
DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that…
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene…
Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
This study proposes MCEMOL (Multi-Constrained Evolutionary Molecular Design Framework), a molecular optimization approach integrating rule-based evolution with molecular crossover. MCEMOL employs dual-layer evolution: optimizing…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
Nanoscale polymeric thin films are widely used in diverse applications such as energy devices, flexible electronics and biosensors, where a satisfactory mechanical performance is of vital importance to realize their full functionality. It…
With the increasing interplay between experimental and computational approaches at multiple length scales, new research directions are emerging in materials science and computational mechanics. Such cooperative interactions find many…