Related papers: Model for Folding and Aggregation in RNA Secondary…
Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight ~ l^{-c} for loops of length l in the recursion relation for the partition function, we show that the…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
We consider a system of clusters made of elementary building blocks, monomers, and evolving via collisions between diffusing monomers and immobile composite clusters. In our model, the cluster-monomer collision can lead to the attachment of…
The spatial arrangement of components within an mRNA encapsulating nanoparticle has consequences for its thermal stability, which is a key parameter for therapeutic utility. The mesostructure of mRNA nanoparticles formed with cationic…
We develop a thermodynamic description of accumulation-layer heterostructures in which the induced sheet density is partitioned between the near-interface accumulation-layer charge and a complementary screening charge in the surrounding…
We study the effective behavior of random, heterogeneous, anisotropic, second order phase transitions energies that arise in the study of pattern formations in physical-chemical systems. Specifically, we study the asymptotic behavior, as…
A non-linear Penner type interaction is introduced and studied in the random matrix model of homo-RNA. The asymptotics in length of the partition function is discussed for small and large $N$ (size of matrix). The interaction doubles the…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…
Mechanical interactions between biological cells may be mediated by secreted products, making them dependent on the local particle density. Here, we explore the generic physics of density-dependent attractive interactions. We show using…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…
We introduce a new model of aggregation of particles where in addition to diffusion and aggregation upon contact, a single unit of mass can dissociate from a conglomerate. This dissociation move conserves the total mass and leads to a…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
We investigate the competition between two quasispecies residing on two disparate neutral networks. Under the assumption that the two neutral networks have different topologies and fitness levels, it is the mutation rate that determines…
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
Due to the potential applications in biomedical engineering, it becomes more and more important to understand the process of engulfment and internalization of nanoparticles (NPs) by cell membranes. Despite the fact that the interaction…
The aggregation dynamics of slime mold is studied using coupled equations of phase \phi and cell concentration n. Phase waves work as tactic signals for aggregation. Branching structures appear during the aggregation. A stationary branching…