Related papers: RNA folding kinetics using Monte Carlo and Gillesp…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
Recently-proposed particle MCMC methods provide a flexible way of performing Bayesian inference for parameters governing stochastic kinetic models defined as Markov (jump) processes (MJPs). Each iteration of the scheme requires an estimate…
The effect of different Monte Carlo move sets on the the folding kinetics of lattice polymer chains is studied from the geometry of the conformation-network. The networks have the characteristics of small- world. The Monte Carlo move, rigid…
Bridging algorithms are global Monte Carlo moves which allow for an efficient sampling of single polymer chains. In this manuscript we discuss the adaptation of three bridging algorithms from lattice to continuum models, and give details on…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
We address the problem of approximating the posterior probability distribution of the fixed parameters of a state-space dynamical system using a sequential Monte Carlo method. The proposed approach relies on a nested structure that employs…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We propose a novel stochastic algorithm that randomly samples entire rows and columns of the matrix as a way to approximate an arbitrary matrix function using the power series expansion. This contrasts with existing Monte Carlo methods,…
Profiling is a process that finds similarities between different RNA secondary structures by extracting signals from the Boltzmann sampling. The reproducibility of profiling can be identified by the standard deviation of number of features…
We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…
In the context of self-assembly, where complex structures can be assembled from smaller units, it is desirable to devise strategies towards disassembly and reassembly processes that reuse the constituent parts. A non-reciprocal multifarious…
We propose the $S$-leaping algorithm for the acceleration of Gillespie's stochastic simulation algorithm that combines the advantages of the two main accelerated methods; the $\tau$-leaping and $R$-leaping algorithms. These algorithms are…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
Molecular chaperones are ATP-consuming biological machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states for long times. Unassisted folding occurs by the kinetic partitioning…