相关论文: Information-Thermodynamic Analysis of the DNA--RNA…

We examine stochastic processes that are used to model nonequilibrium processes (e.g, pulling RNA or dragging colloids) and so deliberately violate detailed balance. We argue that by combining an information-theoretic measure of…

Protein translocation in cells has been modelled by \emph{Brownian ratchets}. In such models, the protein diffuses through a nanopore. On one side of the pore, ratcheting molecules bind to the protein and hinder it to diffuse out of the…

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…

Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…

Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…

Feedback control uses the state information of the system to actuate on it. The information used implies an effective entropy reduction of the controlled system, potentially increasing its performance. How to compute this entropy reduction…

Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…

We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…

While Kramers' rates have been studied for almost a century, the transition path time between states has only recently received attention. Transition paths between different energy levels are expected to be indistinguishable in shape and…

By controlling in real-time the variance of the radiation pressure exerted on an optically trapped microsphere, we engineer temperature protocols that shortcut thermal relaxation when transferring the microsphere from one thermal…

We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…

We investigate the thermodynamics and transient dynamics of the (unbiased) Ohmic two-state system by exploiting the equivalence of this model to the interacting resonant level model. For the thermodynamics, we show, by using the numerical…

Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…

The transport of nanoparticles (NPs) in polymer networks, as a typical simplified model describing various structures in living systems, is profoundly important in biomedical engineering and nanotechnology. Predicting the effective…

We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…

Safety certification of data-driven control techniques remains a major open problem. This work investigates backward reachability as a framework for providing collision avoidance guarantees for systems controlled by neural network (NN)…

Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…

An antithetical concept, adaptive symmetry, to conservative symmetry in physics is proposed to understand the deep neural networks (DNNs). It characterizes the invariance of variance, where a biotic system explores different pathways of…

Onsager reciprocity $L_{ij}=L_{ji}$ is a cornerstone of near-equilibrium thermodynamics derived from microscopic time-reversal symmetry. We develop a geometric framework in which entropy-weighted reparameterization of thermodynamic response…