Related papers: On the directed tile assembly systems at temperatu…
Tile-based self-assembly systems are capable of universal computation and algorithmically-directed growth. Systems capable of such behavior typically make use of "glue cooperation" in which the glues on at least $2$ sides of a tile must…
We perform non-equilibrium simulations to study heat conduction in two-dimensional strongly coupled dusty plasmas. Temperature gradients are established by heating one part of the otherwise equilibrium system to a higher temperature. Heat…
The recently introduced Thermodynamic Binding Networks (TBN) model was developed with the purpose of studying self-assembling systems by focusing on their thermodynamically favorable final states, and ignoring the kinetic pathways through…
Behaviors of Winfree's tile assembly systems (TASs) at high temperatures are investigated in combination with integer programming of a specific form called threshold programming. First, we propose a way to build bridges from the Boolean…
The connection between self-assembly and computation suggests that a shape can be considered the output of a self-assembly ``program,'' a set of tiles that fit together to create a shape. It seems plausible that the size of the smallest…
The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of…
In this two-part study we investigate the phase behaviour of a fluid spatially confined in a semi-infinite rectangular pore formed by three orthogonal walls and connected to a reservoir maintaining constant values of pressure and…
We present new simulation results for the specific heat in a classical model of a binary mixture glass-former in two dimensions. We show that in addition to the formerly observed specific heat peak there is a second peak at lower…
Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is…
Simulated annealing is an effective and general means of optimization. It is in fact inspired by metallurgy, where the temperature of a material determines its behavior in thermodynamics. Likewise, in simulated annealing, the actions that…
A general method for computing derivatives of solution fields and other simulation outputs, with respect to arbitrary input quantities, is proposed. The method of automatic differentiation is used to carry out differentiation and propagate…
The fixed point construction is a method for designing tile sets and cellular automata with highly nontrivial dynamical and computational properties. It produces an infinite hierarchy of systems where each layer simulates the next one. The…
We propose a way to properly interpret the apparent thermal conductivity obtained for finite systems using equilibrium molecular dynamics simulations (EMD) with fixed or open boundary conditions in the transport direction. In such systems…
The theory of computation is based on abstract computing automata which can be classified into a three-class hierarchy: Finite Automata (FA), Push-down Automata (PDA) and the Turing Machines (TM). Each class corresponds to grammar/language…
We consider staged self-assembly systems, in which square-shaped tiles can be added to bins in several stages. Within these bins, the tiles may connect to each other, depending on the glue types of their edges. Previous work by Demaine et…
Self-assembly is a fundamental 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. Algorithms for…
We consider the Dirichlet-Neumann iteration for partitioned simulation of thermal fluid-structure interaction, also called conjugate heat transfer. We analyze its convergence rate for two coupled fully discretized 1D linear heat equations…
We address a fundamental problem for the advance of phononics: the search of a feasible thermal diode. We establish sufficient conditions for the existence of thermal rectification in general graded materials. By starting from simple…
In a previous paper [Physical Review B \textbf{103}, 035417 (2021)], we showed that the equilibrium molecular dynamics (EMD) method can be used to compute the apparent thermal conductivity of finite systems. It has been shown that the…
Multi-component self-assembly mixtures offer the possibility of encoding multiple target structures with the same set of interacting components. Selective retrieval of one of the stored structures has been attempted by preparing an initial…