相关论文: A two stage model for quantitative PCR

The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…

Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with…

After collecting data from observations or experiments, the next step is to build an appropriate mathematical or stochastic model to describe the data so that further studies can be done with the help of the models. In this article, the…

An innovative method is proposed to generate configurations of coarse grained models for polymer melts. This method, largely inspired by chemical ``radical polymerization'', is divided in three stages: (i) nucleation of radicals (reacting…

The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…

We propose a quantum tomography (QT) approach to retrieve the temporally evolving reduced density matrix in elecotronic state basis, where the populations and coherence between ground state and excited state are reconstructed from the…

Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…

We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the Pumping-Quantization Theorem (PQT) that identifies the conditions for robust integer quantized behavior of a…

The step-growth polymerisation of a mixture of arbitrary-functional monomers is viewed as a time-continuos random graph process with degree bounds that are not necessarily the same for different vertices. The sequence of degree bounds acts…

Irreversible and rejection-free Monte Carlo methods, recently developed in Physics under the name Event-Chain and known in Statistics as Piecewise Deterministic Monte Carlo (PDMC), have proven to produce clear acceleration over standard…

The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…

We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…

Stochastic reaction-diffusion models are employed to represent many complex physical, biological, societal, and ecological systems. The macroscopic reaction rates describing the large-scale kinetics in such systems are effective,…

A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and…

We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical invariance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular,…

Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…

RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the…

Many research fields, reaching from social networks and epidemiology to biology and physics, have experienced great advance from recent developments in random graphs and network theory. In this paper we propose to view percolation on a…

We present a kinetic model of crystal growth of polymers of finite molecular weight. Experiments help to classify polymer crystallization broadly into two kinetic regimes. One is observed in melts or in high molar mass polymer solutions and…

Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…