Related papers: Protocols for copying and proofreading in template…
The rotation of trapped molecules offers a promising platform for quantum technologies and quantum information processing. In parallel, quantum error correction codes that can protect quantum information encoded in rotational states of a…
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
Translation is a crucial step in gene expression. During translation, macromolecules called ribosomes "read" the mRNA strand in a sequential manner and produce a corresponding protein. Translation is known to consume most of the cell's…
The theory of multistate template-directed reversible copolymerization is developed by extending the method based on iterated function systems to matrices, taking into account the possibility of multiple activation states instead of a…
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…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
Currently, identification of crystallization pathways in polymers is being carried out using molecular simulation-based data on a preset cut-off point on a single order parameter (OP) to define nucleated or crystallized regions. Aside from…
We propose a bio-inspired sequential quantum protocol for the cloning and preservation of the statistics associated to quantum observables of a given system. It combines the cloning of a set of commuting observables, permitted by the…
Structured matrices, such as those derived from Kronecker products (KP), are effective at compressing neural networks, but can lead to unacceptable accuracy loss when applied to large models. In this paper, we propose the notion of doping…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The proposed framework combines the two fundamentally different classical…
Stochastic approximation is a framework unifying many random iterative algorithms occurring in a diverse range of applications. The stability of the process is often difficult to verify in practical applications and the process may even be…
Combinatorial samplers are algorithmic schemes devised for the approximate- and exact-size generation of large random combinatorial structures, such as context-free words, various tree-like data structures, maps, tilings, RNA molecules.…
Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We study model-agnostic copies of machine learning classifiers. We develop the theory behind the problem of copying, highlighting its differences with that of learning, and propose a framework to copy the functionality of any classifier…
Multi-document summarization entails producing concise synopses of collections of inputs. For some applications, the synopsis should accurately synthesize inputs with respect to a key aspect, e.g., a synopsis of film reviews written about a…
Copies have been proposed as a viable alternative to endow machine learning models with properties and features that adapt them to changing needs. A fundamental step of the copying process is generating an unlabelled set of points to…
We study the activated motion of adsorbed polymers which are driven over a structured substrate by a localized point force.Our theory applies to experiments with single polymers using, for example, tips of scanning force microscopes to drag…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…