Related papers: A phase transition in energy-filtered RNA secondar…
We study wave propagation through a one-dimensional array of subwavelength resonators with periodically time-modulated material parameters. Focusing on a high-contrast regime, we use a scattering framework based on Fourier expansions and…
The increasing interest in the Mueller density-matrix-functional theory has led us to a systematic mathematical investigation of its properties. This functional is similar to the Hartree-Fock functional, but with a modified exchange term in…
Depinning of nanoscale magnetic textures, such as domain walls, vortices and skyrmions, is of paramount importance for magnetic storage and information processing. We measure time-resolved magnetic switching statistics of an individual,…
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…
In this paper, we consider limit laws for the model, which is a generalisation of the random energy model (REM) to the case when the energy levels have the mixture distribution. More precisely, the distribution of the energy levels is…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
The pattern of radiation energy deposition in substances at the microscopic level of lattice, molecule size, or the cell's nucleus is not uniform. The energy of radiation is transferred to the substance medium in the form of discrete,…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…
The recent discovery of a connection between Transformers and Modern Hopfield Networks (MHNs) has reignited the study of neural networks from a physical energy-based perspective. This paper focuses on the pivotal effect of the inverse…
Phase field evolutions are obtained by means of time discrete schemes, providing (or selecting) at each time step an equilibrium configuration of the system, which is usually computed by descent methods for the free energy (e.g.staggered…
In materials that undergo martensitic phase transformation, macroscopic loading often leads to the creation and/or rearrangement of elastic domains. This paper considers an example {involving} a single-crystal slab made from two martensite…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
The derivation of density functional energies from the random phase approximation of self-consistent mean field theory is generalized and applied to a binary blend of diblock copolymers and homopolymers. A nonlocal transformation is…
We discuss a model in which a quantum particle passes through $\delta$ potentials arranged in an increasingly sparse way. For infinitely many barriers we derive conditions, expressed in terms ergodic properties of wave function phases,…