Related papers: Finite-temperature local protein sequence alignmen…
We employ the numerical linked-cluster expansion to study finite-temperature properties of the uniform cubic lattice Hubbard model in the thermodynamic limit for a wide range of interaction strengths and densities. We carry out the…
This paper is devoted to numerical simulations of the short-term behavior of the spatial temperature distribution in a geothermal energy storage. Such simulations are needed for the optimal control and management of residential heating…
We propose a model-agnostic, progressive test-time energy adaptation approach for medical image segmentation. Maintaining model performance across diverse medical datasets is challenging, as distribution shifts arise from inconsistent…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
Quantum phases at zero temperature can be characterized as equivalence classes under local unitary transformations: two ground states within a gapped phase can be transformed into each other via a local unitary circuit. We generalize this…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The relation between collective modes and the phase transition in low density nuclear matter is examined. The dispersion relations for collective modes in a linear approach are evaluated within a Landau-Fermi liquid scheme by assuming…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Machine-learning models that learn from data to predict how protein sequence encodes function are emerging as a useful protein engineering tool. However, when using these models to suggest new protein designs, one must deal with the vast…
In this study, variations with respect to temperature of the increments of enthalpy and Gibbs energy, arising in the dissolution of proteins in water, have been investigated by the methods of statistical thermodynamics. In this formalism,…
We study fragmentation of small atomistic clusters via molecular dynamics. We calculate the time scales related to fragment formation and emission. We also show that some degree of thermalization is achieved during the expansion process,…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…
This thesis presents original results in two domains of disordered statistical physics: logarithmic correlated Random Energy Models (logREMs), and localization transitions in long-range random matrices. In the first part devoted to logREMs,…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…
After the discovery that fixed points of loopy belief propagation coincide with stationary points of the Bethe free energy, several researchers proposed provably convergent algorithms to directly minimize the Bethe free energy. These…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
We consider an arbitrary translationally invariant chain model with nearest neighbors interaction and satisfying periodic boundary condition. The approach developed here allows a thermodynamic description of the chain model directly in…
Within a semi--infinite thre--dimensional lattice gas model describing the coexistence of two phases on a substrate, we study, by cluster expansion techniques, the free energy (line tension) associated with the contact line between the two…