Related papers: Dynamical versus statistical mesoscopic models for…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
The time evolution of the thermally activated decay rates is considered. This evolution is of particular importance for the recent nanoscale experiments discussed in the literature, where the potential barrier is relatively low (or the…
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
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…
The objective of this thesis is to advance the understanding of complex physical phenomena through the lens of statistical physics. Specifically, it addresses two fundamental questions: What types of interactions can induce buckling of…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
Periodic patterns in dynamical behaviours of biological models described by simple form differential delay equations are studied. Mathematical models are given by a class of scalar delay differential equations with a multiplicative time…
We consider the problem of metastability for stochastic reversible dynamics with exponentially small transition probabilities. We generalize previous results in several directions. We give an estimate of the spectral gap of the transition…
Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport,…
We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase…
Deviations of molecular shapes from spherical symmetry may give rise to a variety of novel phenomena, including their dynamic behavior. It has recently been predicted [Mazza \textit{et al}. Phys. Rev. Lett. \textbf{105}, 227802 (2010)] that…