Related papers: Fast, approximate kinetics of RNA folding
Structure predictions of helical membrane proteins have been designed to take advantage of the structural autonomy of secondary structure elements, as postulated by the two-stage model of Engelman and Popot. In this context, we investigate…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
The Fourier spectrum at a fractional period is often examined when extracting features from biological sequences and time series. It reflects the inner information structure of the sequences. A fractional period is not uncommon in time…
European efforts to boost competitiveness in the sector of space services promote the research and development of advanced software and hardware solutions. The EU-funded HERMES project contributes to the effort by qualifying…
Finite mixture models are fitted to spherical data. Kent distributions are used for the components of the mixture because they allow considerable flexibility. Previous work on such mixtures has used an approximate maximum likelihood…
Accurate modeling of magnetic hysteresis is essential for high-fidelity power electronics device simulations. The transient hysteresis phenomena such as the ringing effect and the minor loops are the bottleneck for the accurate hysteresis…
The Milestoning algorithm created by Ron Elber et al. is a method for determining the time scale of processes too complex to be studied using brute force simulation methods. The fundamental objects implemented in the Milestoning algorithm…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
We present a dual optimization concept of predicting optimal sequences as well as optimal folds of off-lattice protein models in the context of multi-scale modeling. We validate the utility of the recently introduced hidden-force Monte…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Exploiting symmetries in tensor network algorithms plays a key role for reducing the computational and memory costs. Here we explain how to incorporate the Hermitian symmetry in double-layer tensor networks, which naturally arise in methods…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
Hybrid Optimization Software Suite (HOSS), which is a combined finite-discrete element method (FDEM), is one of the advanced approaches to simulating high-fidelity fracture and fragmentation processes but the application of pure HOSS…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
We discuss R package SQUAREM for accelerating iterative algorithms which exhibit slow, monotone convergence. These include the well-known expectation-maximization algorithm, majorize-minimize (MM), and other EM-like algorithms such as…
The information-encoding molecules RNA and DNA form a combinatorially large set of secondary structures through nucleic acid base pairing. Thermodynamic prediction algorithms predict favoured, or minimum free energy (MFE), secondary…