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Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…

Materials informatics offers a promising pathway towards rational materials design, replacing the current trial-and-error approach and accelerating the development of new functional materials. Through the use of sophisticated data analysis…

In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…

Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…

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…

In this paper we demonstrate the power of a model of tile self-assembly based on active glues which can dynamically change state. We formulate the Signal-passing Tile Assembly Model (STAM), based on the model of Padilla, Liu, and Seeman to…

We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…

DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…

The fabrication of nanomaterials involves self-ordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on…

The number of distinguishable inherent structures of a liquid is the key component to understanding the thermodynamics of glass formers. In the case of hard potential systems such as hard discs, spheres and ellipsoids, an inherent structure…

Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…

Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…

Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…

The nature of distributed computation has often been described in terms of the component operations of universal computation: information storage, transfer and modification. We review the first complete framework that quantifies each of…

We show the first non-trivial positive algorithmic results (i.e. programs whose output is larger than their size), in a model of self-assembly that has so far resisted many attempts of formal analysis or programming: the planar…

We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…

Physics-constrained data-driven computing is an emerging computational paradigm that allows simulation of complex materials directly based on material database and bypass the classical constitutive model construction. However, it remains…

Self assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in…

To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…

DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…