相关论文: A two stage model for quantitative PCR
A chemical reaction mechanism (CRM) is a sequence of molecular-level events involving bond-breaking/forming processes, generating transient intermediates along the reaction pathway as reactants transform into products. Understanding such…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
We estimate the probability regarding polymerization of a macromolecule which is made of distinct monomers. The lattice model of the random walk has been used to mimic the conformations of an ideal chain in two and three dimensions. It has…
Experimental designs with hierarchically-structured errors are pervasive in many biomedical areas; it is important to take into account this hierarchical architecture in order to account for the dispersion and make reliable inferences from…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor utilizing chemical energy input. The time it spends at each…
Quantum circuits that generate coherent superpositions of stochastic processes are key to many downstream quantum-accelerated tasks, such as risk analysis, importance sampling, and DNA sequencing. However, traditional methods for designing…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
Probabilistic model checking for systems with large or unbounded state space is a challenging computational problem in formal modelling and its applications. Numerical algorithms require an explicit representation of the state space, while…
We describe a class of growth algorithms for finding low energy states of heteropolymers. These polymers form toy models for proteins, and the hope is that similar methods will ultimately be useful for finding native states of real proteins…
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected…
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have…
The development of high-efficiency porous catalyst membranes critically depends on our understanding of where the majority of the chemical conversions occur within the porous structure. This requires mapping of chemical reactions and mass…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
Characterizing complex many-body phases of matter has been a central question in quantum physics for decades. Numerical methods built around approximations of the renormalization group (RG) flow equations have offered reliable and…