相关论文: Evolutionary advantage of directional symmetry bre…

Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…

We propose a general design strategy based on genetic optimization to realize asymmetric reflectivity in periodic and non-periodic planar structures containing dielectric and gain-loss layers. By means of an optimization algorithm, it is…

This paper uses the recent idea that the fundamental haploid-diploid lifecycle of eukaryotic organisms implements a rudimentary form of learning within evolution. A general approach for evolutionary computation is here derived that differs…

DNA polymerases are an essential class of enzymes or molecular motors that catalyze processive DNA syntheses during DNA replications. A critical issue for DNA polymerases is their molecular mechanism of processive DNA replication. We have…

This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…

Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…

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…

Capillary thinning of polymeric fluids is central to biological and industrial processes, yet the mechanisms governing thinning dynamics remain unresolved, especially for semi-flexible polymers. Using ideal solutions of semi-flexible DNA,…

We present a novel framework for chemical learning based on Competitive Dimerization Networks (CDNs) - systems in which multiple molecular species, e.g. proteins or DNA/RNA oligomers, reversibly bind to form dimers. We show that these…

At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…

Recent discoveries of gravitational wave sources have advanced our knowledge about the formation of compact object binaries. At present, many questions about the stellar origins of binary neutron stars remain open. We explore the evolution…

DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…

The tendency of repeating past choices more often than expected from the history of outcomes has been repeatedly empirically observed in reinforcement learning experiments. It can be explained by at least two computational processes:…

Reptation theory has been highly successful in explaining the unusual material properties of entangled polymer solutions. It reduces the complex many-body dynamics to a single-polymer description where each polymer is envisaged to be…

We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…

In this work, a neural network is trained to replicate the code that trains it using only its own output as input. A paradigm for evolutionary self-replication in neural programs is introduced, where program parameters are mutated, and the…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

Taking inspiration from biological evolution, we explore the idea of "Can deep neural networks evolve naturally over successive generations into highly efficient deep neural networks?" by introducing the notion of synthesizing new highly…

The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…