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There is growing interest in promoting deformation twinning for plasticity in advanced materials, as highly organized twin boundaries are beneficial to better strength-ductility combination in contrast to disordered grain boundaries.…
Modern systems exhibit unprecedented complexity due to their increased scale, interconnectedness, and the heterogeneity of their digital and physical components. In response to scaling challenges, the system of systems paradigm proposes…
We investigate the entanglement properties of multiparticle systems, concentrating on the case where the entanglement is robust against disposal of particles. Two qubits -belonging to a multipartite system- are entangled in this sense iff…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Coagulation-fragmentation processes describe the stochastic association and dissociation of particles in clusters. Cluster dynamics with cluster-cluster interactions for a finite number of particles has recently attracted attention…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…
Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced exons become alternative cassette exons…
{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the…
The buckling of elastic bodies is a common phenomenon in the mechanics of solids. Wrinkling of membranes can often be interpreted as buckling under constraints that prohibit large amplitude deformation. We present a combination of analytic…
Squeezed states of spin systems are an important entangled resource for quantum technologies, particularly quantum metrology and sensing. Here we consider the generation of spin squeezed states by interacting the spins with a dissipative…
The concept of structured occurrence nets is an extension of that of occurrence nets which are directed acyclic graphs that represent causality and concurrency information concerning a single execution of a distributed system. The formalism…
Concurrent Constraint Programming (CCP) is a declarative model for concurrency where agents interact by telling and asking constraints (pieces of information) in a shared store. Some previous works have developed (approximated) declarative…
Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic…
The theory of spin models intersects with condensed matter physics, complex systems, graph theory, combinatorial optimization, computational complexity and neural networks. Many ensuing applications rely on the fact that complicated spin…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
A complex system is a system composed of many interacting parts, often called agents, which displays collective behavior that does not follow trivially from the behaviors of the individual parts. Examples include condensed matter systems,…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…