Related papers: Finite-temperature local protein sequence alignmen…
A new method to simulate probability distributions in regions where the events are VERY unlikely (e.g. p ~ 10^{-40}) is presented. The basic idea is to represent the underlying probability space by the phase space of a physical system. The…
Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the…
The gapped local alignment score of two random sequences follows a Gumbel distribution. If computers could estimate the parameters of the Gumbel distribution within one second, the use of arbitrary alignment scoring schemes could increase…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
Linear programming is used as a standard tool for optimising unit commitment or power flows in energy supply systems. For heat supply systems, however, it faces a relevant limitation: For them, energy yield depends on the output…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
We show how to achieve lattice-spacing independent results in numerical simulations of finite-temperature stochastic scalar field theories. We generalize the previous approach of hep-lat/9607026 by obtaining results which are independent of…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
The parallel dynamics of the fully connected Blume-Emery-Griffiths neural network model is studied for arbitrary temperature. By employing a probabilistic signal-to-noise approach, a recursive scheme is found determining the time evolution…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
For semantic segmentation, label probabilities are often uncalibrated as they are typically only the by-product of a segmentation task. Intersection over Union (IoU) and Dice score are often used as criteria for segmentation success, while…
We propose a new mathematical tool for the study of transport properties of models for lattice vibrations in crystalline solids. By replication of dynamical degrees of freedom, we aim at a new dynamical system where the "local" dynamics can…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…