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Mesoscale behavior of polymers is frequently described by universal laws. This physical property motivates us to propose a new modeling concept, grouping polymers into classes with a common long-wavelength representation. In the same class…
Herein an alternative model to reptation to describe concentrated polymer dynamics is developed. The model assumes that the chains act as blobs that are able to diffuse past each other in a compressed state. Allowing that the local…
We propose a novel definition of life in terms of which its emergence in the universe is expected, and its ever-creative open-ended evolution is entailed by no law. Living organisms are Kantian Wholes that achieve Catalytic Closure,…
The emergence of self-replication and information transmission in life's origin remains unexplained despite extensive research on the topic. A hypothesis explaining the transition from a simple organic world to a complex RNA world is…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
Polymers are candidate materials for a wide range of sustainability applications such as carbon capture and energy storage. However, computational polymer discovery lacks automated analysis of reaction pathways and stability assessment…
The origin of life is often approached through the lens of replication, heredity, or molecular specificity. This paper proposes a thermodynamic framework in which the emergence of life is driven by the persistence of reaction pathways that…
Deep learning models are gaining popularity and potency in predicting polymer properties. These models can be built using pre-existing data and are useful for the rapid prediction of polymer properties. However, the performance of a deep…
This chapter is an overview of foundational results in the mathematical theory of replicator systems. Its primary aim is to provide a unified framework for the mathematical formalisation of evolutionary processes in the spirit of…
Life uses non-equilibrium mechanisms to create ordered structures not attainable at equilibrium; the resulting order is assumed to provide functional benefits that outweigh costs of time and energy needed by these mechanisms. Here, we show…
We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The emergence of membranous compartments (protocells) with encapsulated genetic material was a crucial step life's origin and evolution. The hot spring hypothesis for the origin of life suggests that protocells could have formed in hot…
A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…
Protein sequence generation for engineering requires samples that are biophysically plausible and, when targeting a family/domain, remain recognizable members while exploring within-family diversity. Current discrete generative models…
The question of the onset of the homochirality on prebiotic Earth still remains a fundamental question in the quest for the origin of life. Recent works in this field introduce the concept of recycling, rather than the traditional open-flow…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…